I took a Cutlass Black out for a spin to see the new interior ship damage animations. By the time persistent universe alpha features are complete, we'll be able to make minor repairs on board. Once you get out of harm's way you'll need to take the ship to a repair station or find a player with dedicated repair ship such as the Crucible to fix it. There's no automagical healing/repair of anything in Star Citizen - not ships or players. The permanency of damage is what adds lasting consequences to Star Citizen.