Of course stores could sell digital codes for the NX, but that's not the problem. The problem is convincing everyone that still prefers physical releases (basically the majority of people) into buying a system that's digital only. Either you manage to get Steam-like prices or you risk yourself to abysmal failure. The market is nor ready for a digital-only console yet, and Nintendo is the one company that shouldn't be risking with that.
I still think Nintendo won't do that, though. Cartdridge-based console, yes. Digital only, no.