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Didn’t Nintendo get in trouble before for using a publicly available emulator (and stolen code for said emulator) for one of their console eshops?
Think you might be mixing together a few things: the ROMs on the Virtual Console with iNES headers (already mentioned) and an unrelated third-party developer using mGBA in a commercial game without providing credit or complying with the license. In the latter case, they did end up complying in the end.
I had actually not heard of the second case, it was Nintendo’s roms I was thinking of
