Probably too late to be in the NX if they're just patenting it now.
This particular application was filed in February of this year as a
WIPO international patent application, which means it was likely filed in Japan even earlier.
Beyond that, it is very likely that the majority of patents that pertain to the NX have not yet been filed, or have been filed only recently, or have been filed with non-disclosure requests, because typically Nintendo does not want their actual hardware ideas to become public before they reveal them. See the Wii and Wii U for instance.
That's not to say this application is for the NX, which I personally doubt, but the timing of filing isn't a factor whatsoever in when and where it can be used.
In order to successfully file for a patent (at least according to US law) you must file the patent application within a year of when your invention becomes public knowledge, so if they are keeping certain technologies very secret then they can file the patents for them whenever they wish, such as after, during, or right before they officially reveal the device which will utilize said inventions.