Yeah, I don't think its supposed to work like a vendor. I can't sell items in mine either. And your right the upgrades to the suit are really quite lame. Nothing like the "themes" in FO3. I don't quite remember what the "upgrades" did in the suit....they were super cheap and didn't seem to make much of a difference...correct me if I'm wrong I bought them right away and didn't really check the suit out before I bought them.
They seemed quite useful to me. Workbench, reloading bench, bunch of containers labeled weapons, armor, parts etc...
In fact after the upgrades the only thing the suit lacks is a campfire. And a map marker. 4 loading screens become irritating after a while.