For all we know, the Twelve aren't "real either". Gaius rightfully points out that the manner in which the Twelve were summoned when Dalamud fell was similar to the manner in which Primals (or eikons as he calls them) are summoned. It was the will and faith of people to protect Eorzea that summoned the giant circle, not the Twelve. It merely appeared in the form of the Twelve because that's what manifested as the representation of peoples' faiths. So if we go by this, the only real deities are Hydaelyn, and possibly Zodiark, though we know very little about him.