We know enough, if not everything, based on blog and bits from Alex's posts. It is not rocket science to see possible problems later if nothing else changes.
Currently, restoration is expensive, which means you only do it if the ship is rare or if you have so much money that having a pristine ship now is worth the convenience. Also, for XIV ships, exploiting a bug in which restoring an XIV ship is cheaper than building a new one from Heavy Industry (or buying it from Hegemony).
Next release, we know of story points and how they are earned, and ships can gain built-in mods by spending story points. So far from what it was given, this is the only way to put built-in mods (that you want) on the ship. I guess buying or building a ship will acquire a ship with no additional built-in mods.
Power-hungry players will probably want to keep their souped-up ships as long as possible, possibly forever if they can, if story points are hard enough to grind for. (Currently, endgame player can afford to scuttle and build new ships if convenient. I would not do this if I lose ship with built-in mods, unless I have so many story points that I can spend them painlessly on a new ship.)
Therefore, for the next release, if it is less painful to spend money than story points, then player will either restore the ships, or reload and replay the fight until no ships die if restoration is still too expensive (and story points tedious to gain).