Yes, it was pollinated, strange you only got one flower making seed. There are flowers which can self pollinate, but the onion is not one of them, the pollen is produced before the female part of the flower is ready, so it is only good for other onions that flowered earlier; was this a single early flower by any chance?
will the plant still grow seed that that are inert?
I keep going back to this in my head, I can't think of a plant that does this, but I feel there must be one, nature is like that, it fills all the possibilities, there are plants that grow fruit without seeds, but sterile seeds?