Comes down to how successful the NX proves to be with one very important demographic: children.
Hino has already suggested as to why titles like Layton and Fantasy Life went mobile, because their underlying elements are designed to appeal to older audiences that they feel they cant hit with the 3DS.
If the children demographics moves, largely, away from Nintendo to mobile (there are tons of kids in mobile but enough exist on 3ds to make them a viable demographic) then I think the IP will move along with that.
But we will really need to see how YW3 performs first. And what NX ultimately is.