I'd say that's a feature experimented with Generation 6; ORAS had the Mirage Spots, and ORAS are remakes of Gen 3. Gen 3 offered one of the better implementations of Secret Bases, which were player generated content, and the ORAS games expanded on those with the use of QR codes.
Only time I've gotten counterfeit games is through someone on Facebook Marketplace. I didn't know at the time how to distinguish between genuine and fake Pokemon GBA games. They're getting really close. As for the ROMs, it would only make sense for publishers to enforce copyright law on them if they actually sold them still. Otherwise, illicit ROMs are the best option we have for game preservation in a time when publishers are effectively destroying games by putting DRM in them that bricks them even if legitimately purchased, a la Fable III for Windows.