Hotkey is set during initial controller configuration. You should be able to have a different one for every (type of) controller you use. Configure additional controllers through the EmulationStation start menu.
Edit: oh but I guess you want to do this only for NES, so the shoulder button still works when using the SNES controller for SNES games... maybe not so simple then. The docs do say that hardcoded configurations are "locked to a specific core and controller," but in the example they give, I don't see anything that does tie it to a specific controller.
