Throwback to the NES Classic ROM having a ripper/uploader’s signature in the game code. Because Nintendo didn’t ever bother archiving their own games, and just downloaded ROMs from the same sites they were trying to shut down.
No they have not. If they dumped their own cartridge or had the ROM somewhere in their archives, it would be identical to one downloaded from the Internet. The whole controversy happened because someone saw the iNES headers in whatever release of Super Mario Bros was new at the time. Those headers are added by all NES cartridge dumpers, and the creator of this format developed the NES emulator used by Nintendo in Animal Crossing for the GameCube.
Rom pirates usually trim and sign their releases, specially if they have to break or decode any encryption. These pirate's signatures have been found in official Nintendo releases. Some of their own emulators have also been found to run piracy emulation software. They are pretty much hypocrites.