All evidence currently points to them simply using the format (possibly because they hired an iNES developer way back in the day), not them selling you pirated ROMs.
For one, none of Nintendo's ROM files match any pre-existing ROM files you can find on the internet. [1]
During the gigaleak (an event where Nintendo's internal network was breached and many files were stolen), it was found that Nintendo has a vast archive of master ROMs that they pull from whenever they need to re-release a classic game. While they may use community-dumped ROMs for internal testing, they are highly insistent that they ship their own original copies in retail products. In fact, it was even found that they had a tool to convert from their internal format for storing NES ROMs (CHR and PRG ROM data stored in separate files) to the iNES format. [2]
[1] https://www.reddit.com/r/emulation/comments/uaszvp/no_ninten...
[2] https://luigiblood.tumblr.com/post/682410911082921985/no-nin...
Not just that, Nintendo got caught distributing community ROMs in their own virtual console.