It has been confirmed to Serebii that Pokémon Shuffle, the 3DS title, will shut down on March 31st, 2023. That’s just shortly after the 3DS eShop is being shut down.
It has been confirmed that Pokémon Shuffle is to enter an end of life service for Nintendo 3DS alongside the eShop going offline. Starting March 31st 2023, you will no longer be able to have daily login bonuses or play in the Ranked Stages or obtain Event Stage data if you haven’t already. If you change the date of your device after this, you’ll be unable to play Event Stages as well. You’ll still be able to play standard stages after this.[Serebii]
This is unfortunate news, but it seems that the question of whether or not the service would stay online after the eShop closes next year has been asked before.