Well, consider how large a capital ship really is. Now also consider the amount of damage they take from incoming fire. Realise the huge amount of damaged metal, chunks of whatever material they're built from are blasted off. It would take a nano-bot years to repair that. It just doesn't make sense.
Repair crews inside the ships would be able to repair electronics and other damage, but I'd like to see them get in a space-suit and start to weld new armor onto the ship during combat.
Also, this would require an immense amount of spare armor in a cargo hold. Repair drones has some validity, they can work even in combat, but the limit would be, how much spare armor would the ship carry. Indefinate?
Oh I agree with you, it's always a question of realism, it's the universal companion to games. Nevertheless, there's Auto-repair in the game, so we might as well work with it

Now, it would be nice to expand the auto-repair idea and make it more in-depth. Applying your arguments to counter the fact that auto-repair is feasable, I would suggest that auto-repair works in a very limited fashion during combat (slow regen of hull) while out of combat it would speed up a little bit (not as fast as it is now in Beta 2). For every second auto-repair is functioning out of combat, it takes up "Supply" which the ships take with them, once they are out of Supply, they are unable to repair themselves. The Supply idea can be enlarged to encompass weaponry and maybe even shield effectiveness. To reload Supply, ships simply need to be in orbit of a friendly or owned planet.