I had that trouble for like a month now. I thought it would go away in the first few updates, but I was wrong every time. For some reason, those mods of the ghost shell do not appear. YET, those ghost that had those mods still equipped, still have the mods, but seem to not be able to use them. So my conclusion was: I was too low on a level, but now I am on 7 and it is still there. No matter if a new shell got upgraded, and old shell got upgraded, it does not matter, the bug is everywhere and it is driving me nuts. I know, it may not be a big deal, but it is for me though. Especially when I am on the hunt for exotic armor/upgrade cubes. So I just hope that anyone can help me with this or Bungie is doing something about it.