If the NX is the unified handheld/home console concept I believe it will be SD Card based since the games will need to run on the handheld. In other words, the handheld device will have the game card slot and the home console will communicate with the handheld device (ie. it will have no optical drive). I personally believe that this is what the patent is referring to when we saw a console with no Optical Drive.
Stores selling digital download codes would be a poor replacement for selling physical games. You would never get me in the car to drive out to Best Buy to buy a download card: I might be willing to pick up a couple with the initial purchase of the console since I am already at the store but I would never go back for additional games. Retailers would realize this too and a console that only has download cards would have substantially less shelf presence then a console like the PS4 and XOne that offer both physical and digital. Furthermore, this problem would also create a big issue for Nintendo in terms of selling their Amiibo's. Nintendo wants people to come into stores and buy their Amiibo's on one hand, but on the other they would be telling people to stay at home by requiring digital-only purchases. This is a conflicting message and I don't believe that Nintendo would do this.
No I believe that digital downloads will become a bigger trend, but games will still be offered as physical releases on the NX. SD Cards would also allow for backwards compatibility betwween the NX and the 3DS.
