Layered defenses. It doesn't matter if the lord's prayer doesn't work if you already happen to be in a church and haven't invited vampires in. At that point, the fact that the lord's prayer isn't working doesn't fucking matter. No sensible person is going to forgo one or more of their defenses just to find out if one works by itself.
And if you're already in a church, then yes, it doesn't matter. Problem is that it won't show you whether or not it is useless in those sitautions you're not in a church and did invite a vampire in (because you didn't realize he was a vampire).
Um, right. You're thinking of atheists as perfectly pragmatic, unreligious folk. Atheists can be just as dogmatic, petty and arbitrary as theists. Atheism is not incompatible with religion, either.
What part of "other than those he chose (or she chose) personally" came out in small font?
A Catholic has his personal issues -and- his religion's issues. An atheist just has his issues. He doesn't have a rule that says that ripping pages out of the Bible will add an extra six months to his time in purgatory unless he personally thinks it does for his own bizzare and disturbing reasons.
You're also conflating atheism with educated intelligentsia there, that's not advisable. There are a lot of well educated, smart religious folk (I know a few in person). They will likely also know of warding techniques related to foreign vamps, from pop culture or through other means.
So at what point is this (quoting Frank)
The things that "work" are a seemingly random collection of old European superstitions, Catholic rituals, Gypsy magic, and modern science. You can deny a vampire power recharge from earth by sterilizing it! People who aren't religiously invested are at a huge advantage in that setting. Catholics like Van Helsing not only are preoccupied with doing rituals that seem to be completely ineffective for religious reasons, but are also wracked by guilt when they contemplate using entirely effective rituals in a manner that their religion doesn't approve of. Van Helsing has to get permission from a priests to throw blessed crackers around, while an Atheist would just load and go.
being used, if at all?
If the answer is "we're not doing that, because it sucks.", let's make that clear and move on to "what we doing".
Sure, your biologist training might tell you that rattlesnake venom causes coagulopathy in humans, but how does that work on a vampire - an undead monstrosity that sucks blood to continue its own wretched existance?
It could work just as well, it could work better, it could fail to work. Is there any way to tell until we (rule writers) decide?
Trust in the Emperor, but always check your ammunition.