well... hull mods are things specifically installed to the ship, (like say... bigger magazines), so I think it wouldn't make sense to itemize them whole ("you looted a heavy armor, congratulations!"). That said, having some sort of cost to them may be appealing
example:
heavy armor- costs 15/25/40/75 heavy metal plates and 10/25/35/50 supplies
integrated PD AI - costs 1/1/2/2 AI core, 4/6/8/12 microchips, and 5/15/30/45 supplies
this will be partially refunded when taking off the hullmod, ofc this will require more commodity resources to be in the game first
the system thing I completely agree with. AFAIK the hound just dumps flares out of its backdoor, what's preventing them from dumping guided ones? That should only be a small portion of ship systems though, probably just interchangeable flare reserves and drones, that should be about it. Maybe each ship gets a small choice of systems that they can choose that's still exclusive to their ships with little overlap
example:
wolf: phase skimmer - 5OP, fortress shield - 20OP, secondary phase cloak - 10OP
enforcer: burn drive - 10OP, accelerated ammo feeder - 15OP, maneuvering jets - 15OP
hound: flare launcher - 5OP, bomber drone - 10OP, burn drive (god forbid) - 10OP
this allows greater diversification in ship roles, do you want a wolf to be a fast skirmisher, a sturdy line escort, or a flanking strike frigate? Do you want your enforcer to be a bullhead assault ship, a steady fire platform with great firerate, or a nimble combatant capable of attack and escort? What of your hound, the standard fighter jet of a boat, a small but deadly strike platform, or the fastest blockade runner this side of the sector?
this could be defined on the hull file as a new list that looks like this
compatibleSystems["phaseskimmer", "fortressShield","etc."]
each system can then be defined an OP cost depending on hull size in their file or the csv
then a ship can have its choice of system in the .variant file
ofc it could all be too much for alex to commit to at this point but hey, a man can dream, right?