Although I hav no knowledge on the matter, why is there an assumption that this means the iPhone 5 won't have NFC?
I'd imagine if Apple were to introduce NFC it would do so by bringing on board a few large retailers who would support it and get key recognition at the iPhone 5 event.
Square would still serve a role with smaller businesses and for person to person transactions for a while I'd imagine, on top of which one would assume that square would eventually rely on NFC as well and drop the attachment.
Or maybe Apple would buy them outright - hence the reason to establish this relationship now.
More people have credit/debit cards than smart phones. There is no reason why Square couldn't support NFC eventually, but I think for the next decade, retail purchasing experiences, will involve consumers with credit/debit cards.