Yes, every module on your ship can be repaired. even the super special ones.

So far my experience tells me yes, I have done it a couple of times and pretty much I haven't encounter a module that i haven't been able to repair. So I say: go ahead and go crazy scanning, good luck, hope you get good planets.

I have a random somewhat related question:
You know how all ur modules goes uninstalled if you race change from the +deck one(too lazy to remember/look up the name) to another?
Well, do they lose condition status if that happens?
If no, stop here. If yes:
does the mission # artifacts that are normally perma installed also lose conditions?
if no, stop here, if yes:
Can these things be repaired?

I mean as far as I know everything you can regularly uninstall can be repaired... but those are just weird XD

nothing takes damage from you being over-decked....

and the super special uninstallable modules do not take damage ever.... not even from missing upkeep...

They just stop working until you have fixed the too many modules situation.
Went from Sillixx to Genetarr so I had this problem before.