Arial Black
Adventurer
Q: If the Danish call Settlers of Catan a 'leg', is it subject to the taxes that a 'leg' has in Denmark?
A: Yes.
Q: If the German government considers Scientology not a religion, is it subject to restrictions that religions aren't?
A: Yes.
It turns that what we consider things matters.
Whether you consider such beings 'gods', whether the Danish call a game a 'leg', whether Germany considers Scientology a religion, may affect how you, the Danish or the Germans treat those beings, that game and that 'religion', but it will not actually change what those things are.
If a PC from Toril says he's an 'atheist', what happens to those beings? Absolutely nothing. It may change the PC's behavior, but how? If he keeps his thoughts to himself it just means that instead of 99 gods who don't have him as a worshipper, there are 100. None of these beings will notice.
If he tells everyone that these beings are not 'gods' as he understands the term, their clerics will still get spells.
If he acts against the interests of these beings that people call 'gods', that will affect the world to a greater or lesser extent (probably lesser!), but to what end? What is the cost/benefit scenario? Okay, he will gain loads of enemies with divine magic while being unable to ally with other faiths, but what is the up side? What can he gain? He might get a couple of philosophers to say, 'Yeah, I suppose you're technically correct'; meanwhile clerics still get their spells.
In the real world, realising that you don't believe in the supernatural frees you from doing irrational, possibly harmful, things. But on Toril, you don't have to do anything you don't want to do because you don't have to be pious or even a member of a religion, and your definition of 'god' is neither here nor there. Meanwhile, those beings are still granting spells, still wielding their power and influence, and your unbelief is utterly irrelevant.
Tax clerics if you want, it won't alter those 'gods'.