Balance comes to mind as the biggest concern here, and as said that is mostly a matter of testing. And more testing. Some revision thrown in with a healthy amount of further testing.
The only other problem this may cause is creating a divide in the server population:
Jumpdrives, bases and cloaks and so on are pretty exclusive to those in large groups or who spend a lot of time online. This is okay as these components are either meant for team type use or don't really give an edge on anything, maybe just a new, fancy option that isn't terribly useful for most.
If suddenly modules like these started modifying hard stats on vessels of all types, this creates a divide between the can obtain and cannot obtain players. CAU already does this to some degree, although the payback for going beyond CAU 4-6 is fairly negligible.
Base point is: do I want to spend horrendously long amounts of time in-game to grind out a component so I am not constantly at a disadvantage? No.
However, if the module gives no meaningful advantage, why would anyone spend the time to make one?
I don't dislike the idea and further customization to ships is awesome, but it should be approached very carefully I think. Not everyone on the server has a windfall of cash, and balance should be approached with that in mind.
What may actually work better rather than straight "bonus" add-ons are customization options that are power neutral and give no advantage over a stock layout, but do change how it feels:
The thruster that goes faster but with less charge is a good example.
Shields that restore faster but have less capacity and vice-versa.
Overloaded powercore that fires guns faster, but at less damage (DPS neutral. I don't like fires faster and consumes more energy, will just lead to much shotgunning)