Stay with me.
In Europe during the time of Mozart, composers were incentivized to be prolific by only getting royalties off the first public performance of their works. Now that is not fair today because of course we can losslessy reproduce such things infinitely.
However, Humble Bundles (and really, steam sales and other similar discounts and give-aways) work because the vast majority of the money a game is ever likely to make is early in the revenue cycle. Not 20 or 10 or even 5 years later.
We don't know the revenue Nintendo derives from virtual console sales, but you can be assured that virtually none of it is making it to the creators which is who copyright is designed to protect.