The original atomists, Democritus and Lucretius, for example, held that all that exists are composites of atoms. Today we might replace atoms with quarks or strings (the latter, assuming M-theory is true). However, the gist of the position remains the same. Peter van Inwagen, for instance, holds to mereological nihilism: that no composite material thing really exists. He does, nevertheless, make an exception for living things. I won't get into the details of his arguments, since they are not pertinent to this post. While Peter van Inwagen is either a classical theist or a neotheist, Democritus and Lucretius still believed in polytheism, and a materialistic version at that.
Now, let's assume that mereological nihilism is true: mountains aren't real; they're just composites of quarks arranges in a specific way. What relevance does this have on classical theism? I honestly can't see any relevance. The argument from change, the argument from contingency, the design argument, and the argument from desire are each consistent with atomism, or mereological nihilism specifically. Suppose that mountains really don't exist. Does that mean there is no change? Of course not. Obviously, the classical theist will have to defend the arguments in favor of classical theism, but the point is that atomism does nothing to undermine it.