I think it's because they are under the influence of the devil.
The devil usually likes to keep himself hidden, so that people are duped into believing that he doesn't exist. But for some reason, the devil sometimes likes to make his presence explicitly known. So God sometimes permits him to do this (especially in pop culture), in order that Christians may more readily identify the works of Satan.
Also, I don't know about 666 specifically, but with witchcraft in general I think the devil might be doing it in order to desensitize the general public, in order to further dupe people into thinking that he doesn't exist. Like it used to be that everyone acknowledged witchcraft to be evil, and took it seriously. But these days people take it mostly as fiction, as if there aren't really any witches out there. (And then when they see wicca and stuff being practiced, they think little of it.)
On the human level, I think it's because the satanists explicitly acknowledge themselves to be haters of Christ (and/or haters of Christianity), so they deliberately use the number of the beast in order to get the point across.
Additionally, at least among the atheistic satanists it might be an attempt at mocking the idea that numbers have mystical meaning. To them it's all just pseudoscience and superstition. So they us the number 666 (and, to a lesser extent, 13) as a way of insinuating that Christians are idiots. That's my guess anyway.
