If you are exiting WoW correctly, it should be restoring all of your key bindings when you log out. So, say you have 5 programmed to the first action button on the default Bliz UI... when you log in with nUI, it steals that key binding from Bliz's action bar and uses it for the first button on nUI's bar, so it "feels" just like the default UI. When you log back out, nUI puts that key binding back on Bliz's bar, so if you were to uninstall nUI and log back in, you would see the same key bindings you had before.
If that's not happening, I'm not sure why.
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