iLounge corroborates this report noting that there are no NFC antennas in the iPads and that Apple has not requested certification for NFC functionality from the FCC.
Despite speculation that the NFC chip is for an as-yet-unannounced Apple Pay enabled cash register, a search of the FCC’s device certification database suggests that Apple did not seek certification for any NFC functionality in the iPad Air 2, as it would have needed to do if the chip was to be used for wireless communications. Further, no evidence of an NFC antenna was found inside the iPad Air 2.
Here's how Apple describes the functionality of the 'Secure Element':
With Apple Pay, instead of using your actual credit and debit card numbers when you add your card to Passbook, a unique Device Account Number is assigned, encrypted, and securely stored in the Secure Element, a dedicated chip in iPhone. These numbers are never stored on Apple servers. And when you make a purchase, the Device Account Number, along with a transaction-specific dynamic security code, is used to process your payment. So your actual credit or debit card numbers are never shared by Apple with merchants or transmitted with payment.
We'll let you know if any further information comes to light...