This is because the folks who take the simulation hypothesis as a serious possibility (like Bostrom) also believe we are in a non-interventionist simulation (one without a creator/controller who regularly intervenes to answer prayers, reward worship and so on). They don't seem to care too much about whether there are other simulations somewhere whose creators do intervene. Generally they'd concede the point if pressed (OK, somewhere in the universe of simulations and simulators there are gods, but not around here. Happy?) and then move on.

The main point about "theism" (as opposed to "deism" say) is that God or the gods really affect us. They don't just exist as an abstract debating point: it actually matters to us that they exist.