Nintendo has announced that at the start of next year, credit cards will no longer be supported on the 3DS and Wii U eShops in Japan as of January 18, 2022, and this includes other prepaid IC cards as well.
This being said, all other aspects of the 3DS and Wii U eShops will remain functional for now and if you have a shared balance from the Switch or official eShop cards you will still be able to buy games and Nintendo’s website also supports credit cards.
Nintendo hasn’t yet stated if they will make any changes to credit cards in other territories.