It seems like it does depend on the emulator. The default emulator for SNES games seems to be lr-snes9x-next, which doesn’t detect the controller at all. As a test I switched the emulator to snes9x and for the most part the controller works save some button mappings (start and select don’t work). So I guess the question becomes:
How do I enable the controller both in Emulation Station (when I try to map controllers it doesn’t detect the controller at all) as well as in lr-snes9x-next. My suspicion is that solving in one will solve for everything. Thanks so much for responding with that little hint.