You make some excellent and interesting points, but don't discount the number of smart, competent hacker/technologists who are also ardent believers in specific religions. I believe they are a significant if quiet minority.
I also don't seek out believers to critique them; everyone goes through different paths in their life, and may or may not have reason to question any number of beliefs they've inherited or taken up along the way for whatever reason.
I'm fairly driven to dig down through almost everything, but I also have a friend who comfortably believes all kinds of crazy things with hardly a second thought, because "life is more interesting that way". Dunno what direction he'd go if stricken with a life-threatening illness (I really, really hope he wouldn't treat it with prayer circles, chelated mercury, toxin cleansers, homeopathy, etc..) but his approach hasn't caused any problems I can point to, so I have no argument.
Back to hackers -- the topic of religion doesn't generally come up except possibly in random smalltalk, and never in my career has it become a point of conflict (i.e., company-mandated prayer groups or bible study or something like that). So if there's a quiet religious minority, and an equally-quiet non-religious majority, that seems like it would suit everyone just fine.