OK, I tested out some cheats on F-Zero in CatSFC Plus. They worked.
- Find cheats here. The easiest way to save an individual file is to click on it then use your browser's "Save link as ..." equivalent on the "Raw" link. If you can't figure this out, you could I guess just download the GitHub zip bundle of the entire project and find cheats in the "cht" directory.
- Put your downloaded .cht files wherever on your 3DS SD card (not Gateway or anything, the SD card in your 3DS); there's no default "cheat" directory.
- (Optional, set your cheat directory in Settings > Directory, otherwise you'll have to navigate to your cheats from the root each time.)
- Start up the game you want to cheat in and in the RetroArch Quick Menu, enter Core Cheat Options and select "Cheat File Load". If you can't figure out what to do next you suck.
- Now you should see your list of cheats. Turn on the ones you want (highlight them and press left/right on the d-pad) then hit "Apply Cheat Changes".
- Resume your game, the cheats should now be active.
Caveat: These cheat files were all autogenerated and haven't been vetted as working. Best case scenario, they work, but other scenarios include: they don't work; they don't work and they crash your game; they don't work and they corrupt your save; etc.