FWIW, my initial thought about this was to have the bonuses improve as the ship gains experience - sort of a "feel more attached to the ship" sort of thing. But I think this really needs to be something that feels good to do at loadout time, and "oh I built this in and now I have to wait a long time for the bonus" just doesn't cut it.
Which isn't exactly what's being suggested here, but, the larger point is that I think s-mods should be a fun ship loadout thing. Ships gaining some kind of bonus from being battle-scarred and such is a nice idea, but it seems really difficult to pull off. Either you get random bonuses and some flavor of save-scumming (torpedoing your own ships to battle-scar them, perhaps?
), or it's a grind to feel like your ships are up to snuff. It seems troublesome!