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Atheism isn’t really a belief system by itself. It can refer to a lot of things, including positive atheism (the claim that there is not/cannot be a god/supernatural entity), negative atheism (the lack of belief in a deity due to lack of evidence), the absence of religion and many other things. Militant atheism, on the other hand, definitely counts and is susceptible to all the failings you mentioned.
It’s not called militant atheism, you’re describing anti-theism. I’ve never heard of atheism claiming definitively that there are no deities or higher powers either, just that since there’s no evidence the claims aren’t worth consideration and can be dismissed as nonsense.