Nintendo's Yusuke Amano has explained the reasons behind the lack of an online mode in Star Fox 64 3D, and it's possible the reasons of many 3DS games did not included online mode so far.
"This leads me to think that just making multiplayer parts of existing games playable online isn't enough to create a satisfying experience for users. The popular online games work in lots of things, so they play well online - and if we wanted to satisfy everyone who bought the game, the costs required for including online support would be vast."
Yet it wasn't just a matter of cost. There was also a time issue and the developers decided to prioritize the 3D visuals over online play.