This really isn't that surprising. They used ROMs for the classic games in Animal Crossing. They even had evidence it was from a release group, and not Nintendo's own copies
I really don't understand why this is embarrassing. I don't know the exact setup they have going on. Is it like a kiosk where people can play classic games, or is it a monitor just displaying them? They have their own emulator, Canoe, that they used for the SNES Classic. I don't remember the name of the NES one
Weren't at least some of the games in the Super Mario Collection ROMs? I guess I can see why people would expect a direct port from the company that created it, or original hardware running the original games, but it isn't like Nintendo doesn't already have a track record for this sort of thing