Square will be in trouble if NFC takes off. That is why its coming up with what I think is its main product line, the register. The credit card reader thingy is not where it makes money. Once prople get hooked on the analytics it can hope to add the NFC functionality in and still keep going.
Square seems to be attempting to counter NFC with Card Case[1]. Still requires the merchant to be using Square, but has the upshot of working /now/, with the cards/phones you already have, instead of maybe in a year or two when ISIS gets it's act together.
Square as a company isn't tied to credit card processing. Credit cards just happens to what's popular now. If NFC takes off, the company will run with it. When that happens, the shops just need a new attachment or a device upgrade, the software just works.