#it really looks like the original timelines (when our technology in general wasn't advances like it is now) keep cyborgs in more respect

[cienie-isengardu]

Do you have any theories or explanations on why cyborgs in MK lore are plain useless? In MK9 and MK11 it's shown that to defeat a cyber ninja covered in armor and a lot of advanced weaponry you don't need much force (like Kitana easily decapitating them with her fan) and Sektor is pretty much a useless jobber who lost all his fights, same as Cyrax who in MK9 lost every encounter after being turned into a cyborg.

The easiest explanation of course is game mechanics which simply doesn’t allow them to win, and Cyber Sektor (alongside with Noob Saibot) is the victim of this at least since MK9 (2011). At the same time, the same game mechanics allow a relative normal human to defeat a powerful god(s) and for context, the last time Shinnok was beaten down happened when the Elder Gods battled him eons ago. So yeah, the MK universe doesn’t really follow sensible logic when it comes to fighting abilities. 

As for in-universe explanation, I would go with this reasoning:

The first matter is that members of Lin Kuei weren’t intended to fight in an honorable one on one specifically. Bi-Han was one of the best but his specializations, as we were told in Sub-Zero: Mythologies, was assassination and theft. Of course, Bi-Han was a skilled fighter, otherwise he wouldn’t be hired to take part in the Mortal Kombat Tournament, the same as Cyrax and Sektor. However in his line of job, he was trained to steal and kill from hiding and by any necessary means. The clan’s original motto says We are the Lin Kuei, more stealthful than the night, more deadly than the dawn! putting emphasis on stealth and even MK1’s Lin Kuei, though no longer an assassin clan but still definitely a special forces/ black ops in service of Earthrealm, as before favors this tactic on their missions. 

"Stealth is the only tactic I need!" [Scorpion/Kuai Liang vs Shang Tsung character intro]

The C.I. project was meant to perfect members of Lin Kuei by erasing human flaws, but that does not necessarily mean their original purpose (assassination and theft) changed. Frankly, the Lin Kuei cyborg were effective when it comes down to stealth, as in MK9 they twice successfully managed to approach and catch their target without anyone noticing their presence, as was seen with Smoke (saved only by Raiden’s intervention)

and younger Sub-Zero.

For the record, Cyber Lin Kuei managed to sneak up into Colosseum full of guards, people with special powers including two excellent sorcerer (Shang Tsung and Quan Chi) and Emperor himself. Granted, everyone was focused on Tournament and Kuai Liang’s attempt at murder but that is the point isn’t? Cyborg Lin Kuei had means and experiences with using that kind situation for their benefit.

And let’s not forget Cyber Lin Kuei and Sindel's attack on the heroes. Only Cyber Sub-Zero managed to detect other cyborgs before their attack - most likely due being one of them. Now let’s compare it to Sindel’s attack, when the Earthrealms were warned about by Kitana who senses her mother’s presence. So the Cyborg Lin Kuei  ambush did not fail due to Lin Kuei’s lack of skills but because Earthrealm luckily had a cyborg on their side before they could sneak up and assassinate humans.

Additionally, older source material like Cyrax's bio and ending specifically point out that lack of the soul makes a cyborg undetected:

Mortal Kombat 3: "Cyrax is unit LK-4D4, the second of three prototype cybernetic ninjas built by the Lin Kuei. Like his counterparts, his last program is to find and terminate the rogue ninja Sub-Zero. Without a soul, Cyrax goes undetected by Shao Kahn and remains a possible threat against his occupation of Earth."

Mortal Kombat 3: "Cyrax is captured by Sub-Zero and reprogrammed with new orders: Destroy Shao Kahn. With Kahn unable to detect the assassin's soulless presence, Cyrax delivers a successful sneak attack. But, after eliminating Kahn and saving Earth, Cyrax awaits new orders from his Lin Kuei headquarters. The orders never come and Cyrax malfunctions. He ends up stranded in the middle of a vast desert, blindly heading towards his base."

Also thing worth to keep in mind: Cyber Sektor and Cyrax may lost their fight in MK9, but Cyber Sub-Zero defeated both Goro and Kintaro, Kano and Noob Saibot in almost one go and none of those fighters, especially not Prince Goro, the Champion of Mortal Kombat Tournament, could be called a weakling.

So, one of things constituting the problem may be that Lin Kuei were the most adapted at stealth and ambush attack but once they lost the element of surprise they could lose the fight against more experienced warriors. The clan may have great individual fighters like Sub-Zero brother, Smoke, Cyrax and Sektor, but the average member not necessary must be on the same level as those named warriors (additionally, even those named characters worked in pair for most of time, with Bi-Han being the biggest exception in games however in some older comics he too had a partner, Hydro).

The other disadvantage the cyborgs face is definitely the existence of magic and generally speaking a different “reality” laws between realms, for example - earthrealm technology does not work properly on Shang Tsung’s Island (the best example comes from MK film 1995, in which Sonya’s radio and compass stopped working once she has arrived there but of course, this aspecy varies between sources). The Lin Kuei, as a clan familiar with magic and super powers for ages, probably took into account such a problem, however even the best calculation can’t compare to first hand experiences, so there is a chance in some settings the cyborg technology will be affected by specific factors and maybe even a place itself - here is a good moment to wonder if Kitana’s fans are enhanced by some sort of magic that gives the control over weapon  “against the  laws of physics” during her fatalities? Whether introduced as Shao Kahn or Empress Sindel’s daughter, she is a princess so it is very likely her gear is of the best quality and may be made of either magic material or magically improved when crafted. Such a weapon combined with her skills honed for hundreds of years make her a very dangerous enemy to face. 

Another matters connected to cyborg technology is that MK lore proved 

A) programming may be prone to corruption which definitely affects the cyborgs abilities. This is especially seen with Sektor in original timeline:

Tournament Edition: "Sektor's programming had become corrupted during his many violent battles with Outworld Forces [...].

and

Bio Kard: "One of the original cyborgs manufactured by the Lin Kuei clan, Sektor has grown more and more corrupt over the years. As his programming deteriorates, he becomes a bigger threat than ever. He may prove to be a danger to all, regardless of their alignment.

B) the cyborgization could improve Lin Kuei warriors’ skills yet the programming may as well kill their natural assassin predispositions and human’s ability to adapt. Which is something that Cyrax feared: "I am among those speaking out against the Grand Master's plan. Surgically transform the Lin Kuei into glorified robots? It kills our intuition, our instincts." [MK9] Since some clan members were forced into C.I. Project against their will, their units requested a slave protocol to keep them under control. The survivors of said program or those who managed to elusive the change attempted to destroy Cyber Lin Kuei (and whenever Cyber Cyrax regained control over himself he turned against the robotic Lin Kuei and that happened on a few different occasions). The threat of rebellion forced Cyber Sektor to limitate subordinates’ autonomy, which in result definitely redacted their primal efficiency. This is best seen in Mortal Kombat X comics series, as cloned cyborgs can’t function independently and need a central master to operate.

and would stop working properly if central master (Sektor) was eliminated until they found the replacement

(and there is something to say about Cyber Sektor’s own programing that was supposed to transcend humanity yet he pathologically kept Cyrax around as his second-in-command despite the danger Cyrax poses).

Another matter worth taking into account about events of MK11 (2019) is how the misplaced through time Cyber Lin Kuei needed to update their technology (“The Cyber Lin Kuei factory is modified to your specifications. Production exceeds projections.”), however I feel only once they were used truly in line with their main advantage - stealth. And that most likely happened during the attack on Lin Kuei Temple, as the game made it clear Cyborgs managed to capture Kuai Liang’s men and change into robots. In all other events, like during the attack on the Special Force’s base or the final battle between allied heroes and Kronika’s army? The Cyber Lin Kuei were treated like cannon fodder and it was their number that mattered, not quality. Which I guess adds to the feeling of their incompetence.

So if I was looking for an in-universe explanation why Cyber Lin Kuei is not effective despite the advanced technology, the most sounding answer for me is the mix of above presented reasons. Their main advantage is stealth and lack of souls make them undetectable however this is rarely used these days to fullest while Cyber Sektor’s fear of losing control handicapped their efficiency from within. The less autonomy the cyborgs have, the less capable they are of adapting to the situation (and turning it to their favor). But also, the named fighters that faced the machines are not novice and each are experienced, dedicated to their cause and skilled - in some cases, also equipped with either magic or special powers including controlling elements like electricity, ice and fire that easily can disrupt cyber technology. But the biggest fault definitely lies with how cyber programming limits their natural instincts in favor of maintaining control over enslaved people/machines.