I have no idea why your keybindings would be gone after deactivating nUI. nUI copies your keybindings for its use during play and restores them on exit. Unless you unbound your keys in nUI before exiting, your Blizzard action bars should always reflect your last keybindings if/when nUI is disabled or uninstalled.
I did just reconfirm that before posting this reply.
EDIT: Did you deactivate nUI in game, or log out and disable it?
What people don't get is that I am, ultimately, an artist at heart. My brush has two colors, 1 and 0, and my canvas is made of silicon.