Prominent iOS developer @Chronic seems to indicate in a series of tweets this morning that there is indeed NFC hardware in the iPhone 5 (or at least prototypes), but it perhaps is not set up to be used for payment systems.
all of you annoying doubters of a certain technology being present in the new iPhone, all I will say is: gpio12— Will Strafach (@chronic) September 12, 2012
I have no way of knowing what will be in the production models, but there would be no reason to remove a major technology that was in an EVT— Will Strafach (@chronic) September 12, 2012
clarification: N42AP had NFC. I am assuming that if that's CDMA and N41AP is GSM, they both will have it. no reason for just CDMA to.— Will Strafach (@chronic) September 12, 2012
@stroughtonsmith people don't understand other uses, which is quite annoying. much more than just payments.— Will Strafach (@chronic) September 12, 2012
Just as a note: The iPhone had the capability to use FM RX/TX radio for years, but Apple decided not to enable it for listening to radio stations or even broadcasting to your car stereo for whatever reason. This could be a similar situation.
We will not know for sure until the iPhone is torn down later this month.