Plus, when a game is out of print, any third-party resales don't benefit the original copyright holder anyway. Nintendo doesn't profit off those $120 SoulSilver cartridges for sale on eBay.
Another reason is that retail traditionally took like 30% but if you buy off of PSN or the eShop, now the game company gets that sweet sweet free money, while actual businesses normal human beings can run can't function anymore.