And there's the reason Nintendo isn't doing it. The top priority for them by a massive margin is consistency. The QA they perform for their own products would require an absolutely enormous amount of staff, all for a minuscule payout because there just is not the kind of demand for those games that would justify such a return.
Even if Nintendo wanted to use existing emulators, they wouldn't touch a GPL project like Dolphin anyway. They do use open source libraries in their games but never, ever GPL ones for fairly obvious reasons.
Tomohiro Kawase, the guy who did the Animal Crossing NES emulator, was a part of the emulation community in the 90s and contributed to iNES. It makes sense that he kept using that header format when he started working at Nintendo.
However, if Nintendo had released any NES ROMs with a "DiskDude!" header? Then maybe. AFAIK this never happened though, and the big leak proved that they had a full final (and sometimes post-final or unreleased final) archive with split PRG/CHR, so they didn't need to use DiskDude! ROMs.