Dark matter has a different cognitive status than God, because there is some evidence, albeit inconclusive, that suggests dark matter (from what I understand; IANAP). In contrast, there is no evidence that suggests God, so a claim that God exists would be arbitrary and is therefore rightfully dismissed.
I would say that God is exactly what you are studying when you are looking at dark matter. God is a metaphor for the unknowable ground of being, the mystery that holds us all. The wisdom traditions have been about understanding the patterns of the Universe, in all senses and to provide a mechanism and context to dissolve the idea that something exists as separate from anything else. Theists and Atheists both seem to get it wrong when they argue over the "existence" of God, as Joe Campbell said, it's about understanding how to read a metaphor and experiencing the direct internal subjective experience of reconnection.
