This was a whole year ago, but seems to be interesting so I am going to respond.
While it may be good as an exercise, one does not need to understand every single philosophical position which underlies their beliefs. Just like one does not need books of philosophical discourse to justify their lack of belief in Santa, the same applies for religion.
It is only because religion is popular and there is strong social pressure in many countries for theism is there even so much argumentation for one side or the other to begin with!
On the religious side:
When religious philosophers talk about metaphysics I can never help but roll my eyes. The ontological justification for the existence of a being which none greater can be conceived? Give me a break. There is absolutely no reason to be well read in arguments against the position of atheism as they either end in infinite regress, such as any argument which states that the universe needed a creator. (response: Well who created that which created the universe?)
Or they just try to twist words and concepts such as analyticity to try to 'trick' their way into proving God's existence. (Looking at you Kant!)
On the philosophical justifications for doubt:
While I do like Hume and Nietzsche and other philosophers who justify agnosticism or atheism, respectively in this case, it seems in no way harmful for one to hold atheistic beliefs without being well read in arguments that help justify their belief.
Atheism is a healthy belief that one holds because it saves them the hassle of going through cognitive gymnastics to justify all the inconsistencies of theism with the reality of their everyday lives. (Cognitive dissonance is a powerful force) If someone holds the belief that fruits and vegetables are healthy and one ought to eat a couple servings of each a day for well being, does the fact that the individual in question is not educated in the physiological processes involved on how the metabolized food provides nutrients to the hosts system bare any relevance?
Perhaps if it was controversial that fruits or vegetables are in fact good for you, like it is often contested is the case with atheism, one may have a reason to do some digging to figure out whether or not he should eat them regularly. However, there is very little doubt for the greater epistemic community that these food sources do provide great health benefits. Similarly, there is strong empirical evidence that atheism is in fact healthy. (Less percentage of atheists in prison for example!) Maybe it is because of the fact that many atheists in the past were more educated, as you mentioned, that there are less significant figures in prison and once the "pop atheist" masses find their way into society those rates will change, but until then, I feel the need to say atheism, or agnosticism, is intrinsically healthy and we do not need extensive justification for our beliefs!