I think the big problem is that the really valuable cards are already very old. Pokémon cards have been around for at least 20 years. Even though QR codes were invented in 1994, it took many years before we as consumers actually started using them. The first QR code I saw was probably in 2012. At that time, we only saw it as a simple way to share links with each other. It was only in the last two years that my parents more or less understood the purpose of QR codes.
I naturally agree with you that QR codes can be used to track the supply chain of collector's items. I would even go further and install NFC chips. For example, you could assign an ID to each card and install the NFC chip in it. This would eliminate the problem of having to scan a code. Of course, the problem now is how to protect end consumers from scams, because collectors can now scan the packs before buying them. But that's a whole other issue that I don't want to go into further.