No way of knowing who started posting first, but whatever.
@Thaeris: I reckon it wouldn't be too difficult to store what turrets/subsystems had been destroyed (or how damaged they were). When the player leaves a sector, you'd shove that information into a table somewhere, so you could load it back if the player ever wanted to go back to that area.
From an optimization point of view, however, it might be better to only store info on damage, since most of the sectors will start out undamaged. You could even set it up so that damage slowly "repairs itself" while nobody's looking. That is, record when a sector was last visible, and when it becomes visible again, increase the health of each subsystem based on that. And periodically check the sectors that aren't real (i.e. the list of sectors with damaged subsystems) to see if they can be "cleaned up" (i.e. all the damage is gone); those ones could then be removed from the list of sectors with damaged subsystems.
So that way, stuff stays damaged/destroyed when you come back to it (for the most part), but if you wait a really long time they repair it. And not just an instantaneous repair job, either.
It even makes sense from a realism perspective; they wouldn't try to repair their turrets if they know the turrets are just going to get blown up again in a few seconds (i.e. if there's an enemy fighter nearby ready to lob some torpedoes at it), and it'd take time to get debris out of the way or do whatever else is necessary to repair or replace a damaged or destroyed turret. It's also possible that they've got a bunch of spare turret assemblies on stand-by. It's a bit of a stretch, though.
