It's going to come down to price. The thought of buying one cartridge and being able to play it on two devices sounds nice, but if having a bluray drive and producing blurays is cheaper, Nintendo will have a bluray drive in the NX console. Cross compatibility for all games can be accomplished by other means anyways. For example, a free digital copy for the other device could be included in every new physical purchase of a game. A NX cartridge player isn't out of the question either.
Ultimately, any potential advantage to using the same medium for both systems is a distant second to price.
"Everything we hear is an opinion, not a fact. Everything we see is a perspective, not the truth." -My good friend Mark Aurelius