The nes roms in animal crossing for N64 had the header for the ines emulator. Now, a few years before Nintendo hired a guy who worked on the audio driver for ines, and that tomohiro is credited with lots of emu projects for Nintendo, so it's not impossible that they reused that header idea. In the gigaleak there's a tool that adds the ines header to clean roms.
This said, it's also not impossible that they're taking a peek in other OSS emulators source code, i recall that luigiblood (a guy obsessed in decompiling Nintendo emulators) found traces of 64dd emulator code from pj64 in some Nintendo product, which then was silently removed after he tweeted about that