I agree with Twerkmotor that it shouldn't happen like EVE; a big part of the fun of the game will be trying to keep fighting when people start blowing holes in your ship, and some parts go down. An EVE style system works in EVE only because there are specific limitations on what you can equip to which ship. With a free-form design system like DU, those limitations are hard to implement effectively, and you could break the game with fast armor repair.
That said, I think you still need nanite repair in some form. Here's why: A ship in EVE frequently takes a minute or less to pop, and then the player that died goes to the market and buys a new ship. Costs some ISK, but if you are well funded, you are back in the game almost immediately, playing at the same level you were before (and if you aren't well funded, you shouldn't be doing EVE PvP).
Contrast that with what I understand to be the case in DU: You build a ship from scratch, piece by piece, using materials you gather, over the course of hours, or days, or for large ships and bases, weeks or months. That ship cost a great deal of actively invested player time; an EVE ship is made by a factory while the player is AFK, very little actively invested player time.
In the case of a lost ship, there is a simple solution to this: Implement shipbuilding factories that automate building from blueprints. In combination with a robust economy for raw materials, this allows you to rebuild lost ships as long as you saved a blueprint and have the funds to buy the materials. You might lose some custom tweaks you made after saving blueprints, but that's not too bad.
Where it falls apart is when you escape, or win, but with substantial damage. Say you got your huge battleship into a fight, and killed the other guy, but your ship lost 40% of its systems and structure. Everything is damaged, and you are barely able to limp back to your base. If you don't have some sort of home-base nanite repair factory, are you going to repair every element by hand, at a cost of maybe a dozen hours of game time before your battleship is back to fighting fit? Or are you going to scrap your ship and build a new one from scratch? What about the 60% that is still good? Is that just wasted? Do you disassemble it? Is the disassembly done by hand too? How long will that take?
This problem is why PvP is Space Engineers always sucked: even if you win a fight, you still feel like you lost, because you have to fix the damage you took, in a painful, boring repair process. Without some easy way to fix ships, people will fight less, the fights will hurt more, and even the winners are likely to get bored because victory is rewarded with dull, repetitive repair work. Eventually, people will just start to leave. This leaves a smaller community, and a weaker economy, making the whole game less awesome even for those with the determination to keep rebuilding every time.
Basically, the faster you can fix or replace your ship after a fight, the more fighting people will do. So, if you like fighting, you should probably hope for some kind of nanite repair system.