PokéTransporter operates by sending your Pokémon to Pokémon Bank, which you can then pull into any mainline 3DS Pokémon game. Using PokéTransporter requires an active Pokémon Bank subscription (though that hasn’t been a concern lately due to Bank becoming free), and you could only even download Transporter if you had an active Bank subscription.
So unless Game Freak completely changes the way these apps works, no, PokéTransporter will become defunct. This shutdown will sever the ties between 3DS titles and previous-gen titles.
Sauce: bulbapedia, experience