can't find the link! :(
As far as how it was figured out, IIRC people disassembled the VC packages and found the iNES roms in there. iNES is the standard (and an awful) format for NES roms on the internet. it has a bunch of problems and like 20 different new standards have been suggested to deal with with them but never caught on. so iNES remains the standard and the community complains about it periodically. it's not something Nintendo could accidentally replicate, and the iNES headers attached to the rom are proof that they're downloading roms off the internet and packaging them into an in-house emulator. the VC download will include the rom and the emulator with whatever hacks are required to make that game run.
they're also not the only ones known to have done it. as discussed in this link, a lot of companies are using formats invented by the internet in their re-releases/classic collections, with file extensions still intact:
http://nesdev.parodius.com/bbs/viewtopic.php?p=50943&sid=a5e59fc7e40266d3fdf66f7f2faf8024It's good for a laugh at least. Unfortunately, what it probably means is that most of these companies don't have master copies sitting around of all their old games, and they actively try to shut down piracy and preservation sites. If they were actually successful a lot of the less popular old stuff could just disappear altogether, except for whatever cartridges people still own.