I'm no expert, but I assume that making a bundle of any kind costs significantly more money than it would have normally. The expectation is that buyers would either A) want a fresh coat of paint for their system or B) don't own the system and want to buy the system along with the game they want to play with it, though that doesn't stop them from buying other games.
Bundles certainly are cheaper for the consumer, but the producer expects that they will sell the consoles primarily, and that, simply by having the console, the consumer will be more likely to buy games for that system. That's how they make money off of a bundle.
Now, with that in mind, especially after the Pokemon bundle, Animal Crossing bundle, and Zelda bundle, I assume that Nintendo would make a Smash bundle for 3DS. Should they? Probably not. I think that the 3DS has enough going for it outside of Smash, and Smash for 3DS isn't as much of a selling point there as it is with the Wii U. The Wii U doesn't NEED the bundle, but it's aching for it. The poorer sales numbers of the Wii U can only go up with the release of Smash, and a bundle would certainly push Wii U sales much more than 3DS sales, I predict.