That seems improbable. Aquinas was a Christian, specifically, a Catholic, so he believed in Jesus and the Trinity. On that view, there are no Gods, there is just the One God, embodied in the Father, Son and Holy Spirit. The idea that "Gods are distributed software installed in the hardware of believers" is not just wrong on that view, it's non-sensical.
Now, I can certainly believe that Aquinas believed that God (singular) acts in humans in a similar manner that human minds act in humans in that both God and human minds (souls) exist in some non-material realm and act on material human bodies in some mysterious way. But that is not the same thing at all. Software does not exist in some spiritual realm that is separate from material reality. There is nothing metaphysically mysterious about software. There is something essentially metaphysically mysterious about God, and almost certainly on Aquinas's view, about minds as well. I am far from being an expert on Aquinas, but I would be shocked to learn that he was not a dualist.