Not really. There's a lot of science that he doesn't understand, but he does seem to be actually interested in understanding things as they really are and generally when an expert explains something to him he gets it.
He's mellowed on the conspiracy theory stuff a lot in recent years, and you'll often see him arguing with his friends (like Eddie Bravo) about his crazy conspiracy ideas. He attributes his new stance on this stuff in part to his show "Joe Rogan Questions Everything" which he went into expecting to find mysteries and just found a bunch of crazy people and fraudsters.
He hasn't completely left the conspiracy theory mindset, but honestly I see him challenging it much more than supporting it these days. The thing I think he's nuttiest about nowadays is that he has bought into the weird ideas of Graham Hancock et. al.
He's often wrong, sometimes excruciatingly so, but when people make a clear case he changes his mind. I think he really is curious about the world and does want to understand what's true, and not just what he would like to be true.