You could maybe use the touchscreen for changing tools in Zelda as well, freeing up the XABY buttons for something else. If the emulator had very flexible input options you could probably figure out some rough solution for most games. The N64 pad always was a bit weird, even when you've got enough buttons it can be difficult to make the controls work unless you have the real pad plugged in.
I reckon it's all academic anyway, really, it's probably a bit much for the Caanoo to handle, and even if it does ever happen it will probably only be a few select games.