While it can't be used in the Switch's N64 emulator, datamines have revealed how Controller Pack support has been present for some time now.

Game consoles typically support a limited number of input devices, meaning that console games are often completely optimized for the default controller supplied with that platform. Nintendo’s… ...

The good news, though, is that the hackers' efforts show that Nintendo Switch Online's N64 emulator does indeed have Controller Pak functionality - it's just not currently enabled on the service.