I don't know about most of these games you've mentioned. All I can say is that prices are high, because certain people are willing to pay them. A game like Earthbound on the SNES can still sell for $500+ even though you can play it on the SNES classic.  So there is more going on than just the availability to play a game.

People collect for a variety of reasons. Some want to play on original hardware, while others like to see a physical copy on their shelf. As long as there are collectors willing to pay these prices, then some games are going to sell for a whole lot.

That how collecting of anything works. You can buy an original painting for big money, or a reproduction for next to nothing.

Few people are willing to pay the big bucks. But, apparently there are enough people who are willing to do those things to support the high prices.