I don't think the secure element is in the Sim card...maybe it is with these phones and maybe not. But I know when people was rooting their devices and attempting to get Google wallet to work on their devices months ago, a lot of people ran into this issue and messed up their NFC where it wouldnt work again and was presented with an " Secure Element" error. And it had nothing to do with the Sim card whatsoever.
Now the Isis Mobile Payment , that requires a different Sim card for that to work.
But I doubt the current Sim cards have anything to do with NFC...