I had 26,000 ish nano crystals when I had completed the game.
When you return to select a mission you get all the enhancements you had at the end of the game but you will be in minus nanocrystals.
I have now got -26,000 nanocrystals as I start picking through missions on super soldier level. So it'llbe a while before I can make use of any other enhancements. (This then starts counting down as you kill the SEPH.
Not the end of the world but I wouldn't have minded plying about with the others during my replays.