There's one little line in this interview that seems. . .suspect.
http://www.wired.com/2016/06/zelda-breath-wild-aonuma-demo
“I’m not going to create something where the users are going to have a different experience,”
Now granted, the previous paragraph is talking about the Gamepad not being used because it's not fun, but why would he say that? It's at least a bit curious.
But there's more than just touch controls to wonder about. All-Star Mode is already about filled up with trophies on that background rack by the time you get to the final section. What if they decide to go for more? How many more characters can they add to that rack before it runs out of room entirely? How many more characters can they add before certain challenges become too difficult? What if they want to up the graphics to show off the power of the NX?
I don't really consider Smash Wii U and 3DS to be "ports" of each other despite sharing a lot of content. A "port" is what I consider to be a game essentially unchanged except for some new items or characters. Even if Smash NX is similar, I think at minimum it will find enough ways to distinguish itself that it will distinctly be it's own version.
Now, if I were in charge of Nintendo. . .I'd have a trailer for an entirely new game up when I announced the NX and have the hype train chug itself along for a while while the game was worked on. But of course I'm not in charge of the company, so I can't exactly have any input on that.