I have visions of RoboCop here. The robot follows it's programming to the letter, and as Nonniemouse points out, does not assess the situation to see if it's actions are a good thing. A robot cannot tell the difference between good and bad! That is a human function, and human instintcs also come into play. I think it was Star Wars IV (or the first one as those of us in our 40s like to call it) where someone utters the immortal line, "Remember they can jam every instrument except your eyes".
When you're in a fight, 'shoot the bad guy' is always the Good option. There's a lot less opportunity for 'good and bad' in actual combat - like I said previously, the only advantage a human has is the ability to disobey orders, and if your AI's decision tree is complex enough, it doesn't matter that it can't break outside of its programmed options. You do not need to pass the Turing Test to shoot a gun, your 'Artificial Intelligence' can in fact be quite stupid (or more accurately, savant-like) as long as it's good in the one thing it needs to be good at. The circumstances that would lead to an interstellar war in the first place are also those likely to result in a war of extermination...there won't be silly concepts like 'civilians' or 'collateral damage' or 'war crimes', only Them and Us. Killing Them is victory, Them Killing Us is defeat.
That is another problem with remote drones. There are a limited number of radio frequencies available. All of which can be jammed by a constant white-noise broadcast!
So your drones fly off, and just keep flying because your control signals aren't getting through...
What control signals? You already established that the drones are limited to lightspeed, and so they can't have human input directing them as that would make them too sluggish to operate. Since we're operating these in an offensive situation, the drones are going to be loaded with their programming before they launch, which would include a 'If cut off via jamming', follow these parameters' routine...we can stick this on modern-day Predator drones, a space fighter is not going to be left helpless by a little white noise. You can't cut the drone off from what it doesn't need to operate. And for all that a human can fly by eye, the Mark One Eyeball is a really awful tool at the speeds and distances we've been assuming as constant through this debate.
Androids.... Now, if we send out a strong enough EMP, it is going to fry every circuit in their brains. Something humans are not vulnerable to. Of course the AI in the human piloted ship is also vulnerable to EMP but not if it is shut down.
So, Glyph, honey, your robot/drone fighter fleet is dead in space, and my pilot/AI combination fighter fleet has just powered back up and breezes past yours, not even bothering to waste ammo on them, and is now in a position to attack your carrier!
So why can your bio-hybrid fighters power down, fire their blast, and power up again, but my drones can't detect you powering down and power down themselves to let the EMP wash over them harmlessly before reactivating and continuing to devastate the poor organic shlubs with their superior weaponry, maneuverability, speed, and armor?
Can you shield your robots against the EMP? Probably, but all that shielding is going to dispose of your weight and volume advantage. My ships have manual controls that don't rely on the AI, so can still be flown, although not as well. And rebooting the AI if it does get EMPed might bring it back on-line. I say might because I don't know but it would be nice if it did.
I'm rather annoyed I didn't think of the EMP earlier in this discussion. The one weapon that electronics are vulnerable to that biologicals are not.
Seriously? EMP hardening is a trivial affair, we've already figured it out with our current technology - it just involves different construction materials, or incorporating a Faraday cage into the outer hull. For that matter, If you're building anything in space at all, you're already being bombarded by tons of constant background radiation. EMP pulses are going to be worse than useless in a stellar combat situation, since the very nature of the environment requires significant advances in the field anyways.
But heck, let's say you somehow manage to build a Better EMP. All you've designed is a short-range burst weapon with exactly the same end-result properties as a weak laser - Speed-of-Light attack speed, and trading damage for a short omnidirectional burst, affected by range due to dispersion. Except you don't have to shut down your own ships to fire the laser, and the defensive measures will be the same - moving to evade or powering down after the incoming attack is detected (your opponent powering down all their electronics is a pretty bit IMMA FIRING MY LAZOR hint) and before the shockwave can reach - a computer will be better and determining the precise speed of propagation of the pulse, and be able to power up its systems immediately after it hits.
And frankly, I'll trade 1 weapon electronics are vulnerable to for the dozens that biologics are vulnerable to. That tonnage you've allocated to an EMP burst device, I'll slap on a directed neutron burst projector and cook your delicate organic meat-sack right through the hull and armor. Or, you know, bigger lasers and just shred your biofighters the conventional way. Or carry the same weapons as you, minus your big bulky EMP generator and the gooey chewy center of your delicious Organic Fighter Pop, and fit two or three times as many drone fighters into the same carrier tonnage.
And for that matter, that's another advantage of a mechanical-based fleet...replacement time. It takes time to gestate and grow new organic pilots, and more time to train them, in addition to building their hardware. Even with mass cloning tanks (and if you've got those, are you really any different for using drones made of meat instead of metal?), cloned organisms still grow at the same rate as normal ones. Comparatively, the drone factories will be able to pump out fully operational ships as fast as the machinery will allow them.