As others have said, there are lines...
Mods that upgrade add value: (well done) LEDs, CDMD, upgraded mechs and boards, Cliffys, Pinsound... a lot of reasonable people do some or all of these things to keep the game working or get it a little more up to date.
Aesthetic mods that can be removed are a wash: molded toys, action figures, translites (if you kept the original)... a new buyer can simply remove them and no harm done.
Aesthetic mods that would be difficult to remove can hurt the value or sell-ability for sure: Custom cabs, armors, decals... if the buyer loves them then good deal but those are often personal preference and may not appeal across the board.