I'll be updating this with my testing, but as of right now, I was able to bring up the overlay and enable Emuiibo. Did you copy the ovlmenu overlay into the /switch folder as well as the nx-ovloader in sxos/titles, and then put the emuiibo folder in titles, and the emuiibo overlay into the /switch folder? if you did all that, did you reboot afterward? I don't have any amiibo on mine at the moment, because honestly I didn't think I'd get this far, but I'm about to transfer some over and start playing with it.
Update:
I loaded an Amiibo, and while I'm able to enable Emuiibo, and attach the amiibo, the same thing that was happening on previous versions is happening for me. When I open BOTW, it gets stuck on the loading screen. It seems the emulation just doesn't work right on SXOS.