Of course they'll release a sequel, and there is no doubt about this.
But Splatoon 1 on NX would have a lot of sense, why you think it won't?
Just look at how many games on Wii U Nintendo has already annunced to port on 3DS, and even how many games are likely gonna be release on NX (Like Smash Bros 4 which is not confirmed yet but seem very likely right now), and look at how much Nintendo is supporting the game.
Nintendo saw that is still selling, and it don't want it to stop, they released a Wii U bundle, which is not much but at this point is all they can do on Wii U, that's why they will port Splatoon on NX, probabily not at launch but in the same year of NX release (2017)
I can see as NX launch line up Zelda, Smash port, and a new Monster Hunter multiplatform with 3DS. They could release Splatoon 1 NX some months after that (or maybe as a holidays game), and then release Splatoon 2 in 2018.