[Wowfunhappy]

The article you linked is about something quite different—Nintendo used a straight dump of their game from the internet. I'm guessing some engineer who didn't know about iNES headers thought they'd save time using the internet versus going through Nintendo's archive.

Newer VC releases haven’t had these headers, by the way. I guess if you were being conspiratorial you could presume Nintendo deleted the headers specifically, but we know it’s not like Nintendo doesn’t save these files. (See things like Star Fox 2; the complete version on the SNES classic was newer than any of the leaked versions.)

I’m really not aware of a time Nintendo has ever used code from a rom hack or emulator.

[ChickeNES]

This has come up before and I recommend reading this comment: https://news.ycombinator.com/item?id=22756156

[Wowfunhappy]

Oh! Yes, thank you, that does make more sense!