A big warning would help. Or if that route isn't good, some sort of new specific defense. I know the whole point of raiders is the ability to bypass defenses, but you always want to have a counter for everything. For cloakers, decloakers. For fast ships, grav turrets. For standard fleet ships, tractors and various turrets. For big ships, your own big ships. For sniping units, radar jammers (that's more an advantage to the AI, since we can't build those, but at least we can capture them). The list goes on. But when you get to Raid Starships, the only real counter seems to be fore-knowing that it's there, and microing all your units on the planet to go after it immediately. It can't be tractored or slowed or tripped up with mines or stopped with forcefields. Since you can't watch all of the battlefield all of the time, they might as well be invisible. You may not even know they were there until you go to build some new units from a fabricator and it's not there any more.
Anyway, if there was some tech we could unlock that specifically countered raiders, I would be quite likely to invest in it. Maybe it could be a made a bit more generalist, since having a unit that's just an anti-raid starship unit doesn't feel very elegant. Maybe some new shield that can't just be shot through that could be applied to irreplaceable things like fabs, power gens, or factories. If said shield was shot, it could send out some kind of warning wave that focuses every turret and ship on the planet on its attacker. Or even pull in ships from nearby planets (maybe for the mark II version). Or maybe some sort of distraction unit that will draw the attention of ships on to itself and if destroyed will counterattack with a one shot powerful barrage of damage on the thing that killed it, while also sending out an alarm message to the human team. If it had a high enough metal/crystal cost and low cap it wouldn't be effective to seed these across every planet, but putting them on worlds with valuable capturables would be a viable strategy. I'm not too worried about something to defend the command station. Although it's annoying to lose this (and to only hear about it because the AI just taunted you) it's not that hard to replace... well unless it's the home station of course.