Humans piloting spacecraft are always going to be inferior to AI.
Humans need life support, protective structures and a whole bunch of other garbage to make them even usable in deep space combat. Not to mention humans tend to think in 2D planes in terms of warfare.
AI on the otherhand does not need life support or any other garbage, and the technology for such machines, isn't even really that scifi. You can also miniaturize AI space craft to be incredibly small given the lack of life support. And given both the 3D nature of space, the lack of obstacles, and zero air resistance Why have a space fighter jet when you can have a engine attached to a laser/missile launcher with an AI controlling it and an excellent IR camera (with out atmospheric distorition, and easy methods of heat dissipation that don't involve radiating heat you are very easy to see with IR cameras in space) making it hard to hit easy to mass produce and easy to manage and automate fights with. Plus you don't have to worry about losing one critical part of the ship and lose the pilot, you can even create redundant AI's. Plus computers have much better reaction times.
In the future it might get to the point you never need a human in the battlefield at all, even to give commands, and abstract battles to the strategic level "Im going to send AI starfighters here to defend this location (the AI's can handle interbattle logistics) and AI's over here to do another thing"
So why am I mentioning this if you are adamant on human pilots? Because you tagged this as science based.
Drones were the primary fighter previously until some advances were made with MMI and biological enhancements. Also, multiple drone hacks were done so the public perception on them dwindled.
Humans are going to be in relatively short supply compared to manufacturing drones, even ignoring the fact that the growth rate of humanity is projected to flatline on earth alone. Enhancing MMI isn't going to solve the rest of the logistical problems with carrying human sized vertebrates in space either, let alone humans themselves.
And if you want to apply reactions of humans like those today to those of tomorrow, they are going to be even less receptive of sending actual humans into space than drones. The outcry of drone striking is significantly less than the outcry against the loss of humans themselves, or even humans yet to even exist!
Plus just because humans are involved doesn't mean they aren't subject to being effected by electronic warfare. You can hack communications very easily giving humans the wrong orders. 898
Any electronics in the space ship are susceptible to hacking as well, if the corresponding drone parts were, and all they need to do is take out lifesupport.
Pilots are very rare and high value, ships will only launch them as a last resort. Each ship usually has a fee gunships (heavy and light) and then a couple fighters. The fighters are more akin to a lighter gunships with automated turrets and AI assistance than a traditional jet fighter.
Why are they launching them like this at all? With AI's you can just have a fleet, with no mothership, no "last resort" needed, every scrap of metal out there can fight. They can even easily be used as fodder, no need for "rare high value ships". You don't want to lose your rare stuff.
Various treaties have limited the use of drones (and other one-use large vehicles) as well as attempted to add responsibility to the fleets to limit debris in space (a large occupation sector in the series relies on scrappers cleaning up space debris).
Space is huge, like really huge. You would have to have trillions of vehicles and constant traffic in a sector with constant fighting for there to even be a noticeable increase in space debree for it to be worth even thinking about cleaning. For a planet it is different, but drones, given, that unlike your assumptions, would be small not large would even be less of a problem, less than your non drone space jets.
Also, treaty limiting use of drones? Why then? Why haven't we already had such a treaty? Drones, unlike WMDs, do not present an existential threat to humanities survival, but rather provide a similar threat to remote missiles, or really any remote kill tech. Drones are just more precise. They are coveted by modern militaries in part due to their public appeal (in the sense that less human deaths on their side take place) and ability to perform warfare with out being there.
No military in their right mind would obey the banned use of drones, even in the modern era, much less the space era. The military would have to simply not exist as we know it, as well as all the knowledge of weapons we currently have. 898