Box art featured on the Canadian EB Games (Disclosure: GameStop is Game Informer’s parent company) website for the 3DS version of Super Mario Maker appears to confirm that the handheld title does not include 3D functionality.
[Source: EB Games]
I'm not sure who would consider this a dealbreaker in any fashion. I tend to use the 3D feature on the 3DS for about 10 minutes each title before the gimmick gets old and I just want to play the game. This won't influence my decision on whether or not to pick up Super Mario Maker 3DS, and I'm fairly certain it won't influence anyone else either.