It would certainly further differentiate ship types, but from a game designer perspective you would be removing a characteristic that can be used to differentiate ship models. At this point I would ask myself "what does this change gives us".
IE: Consider two ships on the present state:
Ship A: Has more Hull Points and less Nanobots.
Ship B: Has less Hull Points but way more Nanos.
From a RP perspective one could say Ship B is easier to repair than A. And yet, if you removed nanobots, both would have the same ammount of HP and... thats it. At the same time, by pushing the change, you would give Freighters a levy over transports (which is always ok by my book).
Granted, my knowledge here is fairly limited so I don't have the math to prove that this would be the case right now, but it seems to me it would make the game shallower on some areas while deepening it in others, so it almost seems arbitrary.
I'll refrain from siding on this, since I just came back to disco, but I was lurking and wanted to add this much.
