I think everyone is underestimating the 3DS and its market base. Let's face it, sadly the Wii U was a flop from the start and hasn't recovered since, and Nintendo shifting focus to the NX isn't exactly the best sign. Meanwhile, the 3DS is dancing circles around the circles it's dancing around the Wii U, PS4 and XBox One combined. From a business perspective, it wouldn't make sense to alienate half, if not more, of the customers, and potential customers, just to appease one fraction of the fans.
I know someone might try to counter this by saying it'd bring more sales to the Wii U, but the truth it, it'd be negligible, if any at all. if Mario Kart and Smash Bros can barely up the system's sales, a single character wont make an impact. Making them exclusive would only doom them to be the lowest selling DLC by simply halving, at least, the market for them.
To compare costs, we're forgetting that for every player to play together, each person must have a 3DS and the copy of the game. While the game is $20 less than its home console counterpart, it has to be sold three more times to have a four-person match. In the long run, the 3DS is the most expensive version, and thus the more profitable in Nintendo's eyes.
I want them in the game very much, they are my second most wanted "character." Is it fair to their fans that they are cut? Absolutely not. But it's even less fair to alienate the 3DS fans by either excluding them or giving them an inferior product as compromise. And with the 3DS by far outselling the Wii U, it's just not a smart idea from a business standpoint.
Personally, I would rather see them "dumb down" Nana to function like Luma or adhere them together like Duck Hunt to make them work. We may lose the ability to desync, but we still keep what makes them special and could make them work. I think that's a compromise all fans can accept.