I think they will give NX all their effort, but we're witnessing a seismic shift in Nintendo's history (and as such in gaming history as a whole), mobile in now going to be a key pillar of their business if not flat out their main pillar.
No way would Pokemon Go have even 1/20th of this reach if it was just a $40 3DS game.
There are kinda two ways this could go
1.) Because mobile is so successful, NX and any other Nintendo hardware merely needs to do "OK" on the market, Nintendo platforms become basically low cost Nintendo-centric platforms maybe where you can also play Android/iOS apps too. Nintendo having their own hardware allows their IP to retain a certain "special" status and allow them to focus their fanbase on certain new IP (like say Splatoon).
or
2.) Nintendo's investors seeing that Nintendo is doing gangbusters on non-Nintendo platforms like iOS and Android may feel that limiting Nintendo IP to Nintendo hardware is limiting their profit potential and may push for broader multi-platform usage of their IP to the widest audience possible.
I could see either happening.
