Yeah I definitely think it is thong, singular. I think it is just common usage though, we do say pair of undies, pants, etc. It sounds right because that's what you're familiar with. Maybe though it's because underpants, trousers, etc. all are 'plural' words, i.e. they have an s on the end that they are referred to as multiple things? Whereas it is thong not thongs, thus, no 'pair of thongs'.
In Aus we call them g-strings mostly. G-string, singular
I can relate LadyZ re shoe thongs rubbing the skin between your toes! I have had that happen so many times. It depends on the make though. For rubber thongs/sandals, Havaianas are really comfortable. I have a pair that I've had for ages that have never ever caused me pain.