As far as CR, spending unspent points should not reduce it. If it's a ship you had in the first place, then restoring it back to whatever it had should not reduce its post-recovery CR.
So for re-equipping ships - well... let's see. It seems like if this was something attained through a skill or a hullmod or whatever, that wouldn't be good - it's essentially a convenience, right, so that generally shouldn't have a cost. At least, it's a convenience in the case of common weapons. For uncommon weapons, it's more of a game-changer, but a positive one.
I think I've just about talked myself into making the base weapon recovery cost for your own ships being 100%. I reserve the right to change it back, though
Currently thinking that the CR, hull, supply cost, and a d-mod are a sufficient penalty for losing a ship, thought it might be a bit weird feel-wise to keep everything else; not entirely sure. If anyone has some thoughts on why that might be a bad (or good) idea, I'm all ears.
... is to make player owned destroyed hulls maintain their settings and configurations.
Oh, hmm - looking at it, it does clear out hullmods and vents/caps, doesn't it. Doesn't seem like there's a real reason to do that; let me make it so those are kept.