I will admit I'm still filling the holes in what I've read of DC unlike how I've read basically everything Marvel.
Anyways, I don't think it has been played for laughs much. I think the whole thing is the result of people mixing up terms like atheist, agnostic, and whatever Bruce Wayne actually is where he knows gods but "It doesn't matter" to him. It's worth noting that in order to have multiple pantheons they had to strip "creator god" status from most of them, DC's cosmology in general is based around the idea of one world's fiction being another's reality. The DC multiverse is just a chain of ideas feeding into each other.
YHVH is the capital G God in the DCU though. Not that other afterlives and such don't also exist.
Just to add onto what you said and what I said earlier, Bob is clearly confusing a
JSA storyline for
Infinite Crisis. Said storyline involves the Spectre (Hal Jordan, and the storyline itself was a lead-in to
Green Lantern: Rebirth) and Mister Terrific having a near-death experience where he sees his wife and unborn son. The even shakes his atheism to the point where he attends a church service with Dr. Mid-Nite, just to give it a try. It didn't stick as he held onto his atheism by
Infinite Crisis.
I believe that Mr. Terrific does acknowledge beings like the Spectre as immensely powerful, but rejects their divinity. For example, both the Spectre and Firestorm can manipulate matter at a subatomic level and transmute elements. However, Firestorm cannot effect living matter with his powers while Spectre has no restriction and even turns Dr. Light into a candle in
Final Crisis: Revelations. Mr. Terrific just sees different magnitudes of power.
As for DC's cosmology, Grant Morrison created a map of the Multiverse where Heaven, New Genesis, and Olympus exist within the Sphere of the Gods. I assume contact with the Orrey of Worlds (the physical multiverse) is limited so the man on the street can be an atheist because the
Justice League and other metahumans in the DC Multiverse are the only ones who have interacted with the Gods and other abstract entities on a regular basis.
I would honestly like to see Bob tackle the subject on
The Big Picture because we all know that he doesn't do research. Hell, I live and breathe DC comics and learn something new when I look into the history of the company and its universe. I learned that one of my assumptions about Hal Jordan/Parallax (that he basically disappeared between
Zero Hour and
Final Night) was erroneous, which is no big deal as learning about something I love is more rewarding than holding to dogmatic beliefs. Bob will never admit that he knows very little about DC or comic books in general and try to pass of his views as the only informed one.