Heh. Not sure how I missed this when it was made. Anyway.
1. I'm not sure why the Thor's and Pantheons and such are even popping up here as an argument. The clear idea is "God" as opposed to gods. Anyone saying something akin to "Hercules exist in Marvel so atheism is completely illogical" isn't grasping the issue enough to contribute meaningfully. The fact that Thor once mused that he didn't know who to pray to is a wonderfully poignant take on it. Same with abstracts and such, who are incomprehensibly powerful, but still clearly limited.
2. Enough ineffable, omnipotent, all-seeing type of entities exist in the comic universes that it would make sense for many of the heroes who are aware of them to be theist, though certainly not of any religion we currently have on our earth.
3. That, however, doesn't rule out atheist tendencies or make them illogical, since a single all-consuming, all-knowing, all-etc. being is hard to pinpoint in either universe, at least from the perspective of most heroes. Even abstracts like Spectre and LT only represent higher forms of power, not "God" in the sense that an atheist would disavow belief in. Even a being who creates a universe, for example, would be that universe's creator but wouldn't be the deific "source" of Creation itself.
4. No more atheists exist in comics than we'd expect from a reasonable pool of people on Earth. About 15-18% of the world's population is non-religious, according to the best census data we have available to us, with anywhere from 2-4% being atheist. Attempts to paint comics as secular, imo, are misleading, as there are far more "neutrals" or those of some faith, than those with a pronounced lack of belief. And if we're to use Mr. Terrific as our guinea pig, he's often undermined by those claiming a belief in a higher power, or forced to scrutinize his beliefs due to outside events, usually without a clear justification of his position. If anything, I see him as much an endorsement of some kind of belief as any overtly religious character. I've read JSA for a long time, and have never seen him as a secular propoganda piece for writers, but rather a mirror for other characters to examine their own beliefs and attitudes. If others believe otherwise, cool, but I'd ask for reasons why that use examples from the comics themselves. Because foils enhance each other's characteristics in writing, so juxtaposing him with Spectre so often is a great way to create character drama. But it could be seen just as easily as an endorsement of theism because of Spectre, but the interpretation lies with the reader...it's impossible to pinpoint a specific agenda from the comics themselves.
5. Speaking of census data, yes, about 1/3 of the world's population is Christian. Whether or not they're practicing is its own matter, but if pressed to label themselves, that's about how many would list themselves as such.
6. I'm atheist, and based on my own justifications for my belief system, I'd still consider myself an atheist in at least the Marvel universe. DC, with their Biblical-style pantheons and frequent refernces to God via characters like Spectre, would be a different matter, as they seem to give numerous characters frequent justification for belief (though the concept of a multiverse and omniverse in both companies throws even some of that under considerable scrutiny). So take from that what you will. It's anecdotal, admittedly so, but used to exemplify the idea that it wouldn't be impossible to justify such a position in either universe.