So, it is useful to assume that Germ Theory is true, but there could be doubt to the reasons why it works?
Sounds like you're now talking about science, and in fact that's how science operates. Science doesn't work on whether or not something is "objectively true", one of the reasons being that people can always dream up some crazy elaborate alternative explanation to some observed phenomenon, maybe something that can't seemingly be disproved. Instead, science bases theories (which aren't the same as hypotheses, but rather models explaining the empirical data) on what withstands the scrutiny of the scientific method. So sure, we operate on the assumption that Germ Theory, Gravitational Theory, Atomic Theory, etc. accurately model what goes on in the real world.
Is your question whether Satanists view Satanism in a similar way? I suppose so. For example, Satanism views humans as animals. I'll go so far as to say that this is an established scientific fact. Even if it turns out that humans aren't animals, and say the Christian creationists are correct that humans were created out of magic by a deity who blew into dirt, or for that matter that the Raelians are correct in their unfounded and ridiculous notion that we're some sort of genetically engineered species sharing no common ancestry with primates, it still wouldn't change the established usefulness of viewing humans as animals and the validity of Satanism for Satanists.
You're not one of those annoying compulsive debater types who visits forums on different religions and tries looking for loopholes, are you? Just checking.