This is a topic I've been harping on for a long time - in theory, your player-character should be able to completely man a ship by himself, since all the NPC's will just be eye-candy when it comes down to actually flying the ship as far as gameplay is concerned. If you, the player, are sitting in the captain's chair and you can then see the whole battlefield around you and fire all your weapons in a satisfying way at targets and fly your ship, you don't need the NPC's, which means you don't need any additional "people" on the ship for it to fly.
...And for that matter, if the ship has such complex AI capability then why are YOU there?
The ship isn't deciding what
to do, you are. NPC ships wouldn't be nearly as interesting as player ships; they would nessecarily be governed by pre-set rules: "Attack ships nearby of X size," "Fly to nearest planet and land," "Follow player and shoot him if he shoots anybody." NPC's (and AI's; since an AI in-game is just another type of NPC) cannot
make interesting choices on their own, players must make them.
In order for a player to control their in-game ship they need an interface, and that interface is usually the keyboard and mouse. If you have to type or talk your orders to your NPC crew to get them to do anything, as you would expect IRL with real crew and you playing a real captain, the interface will be terrible - mis-type and an order won't go through (Yay for 80's technology!), and speech hasn't been implemented in this way before and I would find it slow and clumsy for a game when I'm used to being able to press "W" and my character goes forward or "S" and I go backward. So, if the game uses the very traditional and expected keyboard-mouse interface, I'm expecting that moving the mouse while in control of the ship will make it move or let me issue targets or something simliar, and pressing the keys on the keyboard will let me accelerate/decelerate/roll/pitch/yaw/fire weapons/etc. If that's the case, NPC's are totally meaningless - except
if they are necessary for certain ship components to work properly, and then emulating them at all
times is a waste of CPU. If my ship gets hit and some of them die, then my missiles stopping firing or whatever is fine, but then a hit to my missile bay might disable it without killing the crew, so that's still
possible without emulated NPC-crew.
So at most I would envision that NPC's are used as a kind of limit to how you can build your ship - you need an NPC manning the warp core, and the missile-launcher, and the laser turret; but they don't actually do anything, they just enable that system to work and without them it won't run. I'd go so far as to, when in flight, just estimate what they're doing and their losses (the NPC's are kept as a stat, and a hit to a turret that damages/destroys it has a 50% chance of killing off one of your crew, for example), and some systems might stop working if the NPC stat gets too low. Then I'd actually render them when you're walking around or when you're engaging in boarding actions, though I've expressed how I feel those are overrated for how often they'd probably happen - you'd need to first shoot out an opponent's reactor, weapons, or engines so they can't fight you and can't run, without venting the whole ship into space or leaving it little more than a smoking hulk.