Hmm. I'm not certain, but I think actual vodou priests from West Africa don't do the skull face paint. It seems like more a theatrical addition that popped up as vodou moved from Africa to the Caribbean and then into New Orleans. It could be that the large eyes and labial scales remind them of a skull, of death, or their shifting colors and patterns suggest something not permanent, part of an other world. Creatures seen as liminal are often sources of superstition and mysticism. It isn't only in Africa either.
When I got my first reptile, a Blue Tongue Skink, it took me a bit of work to convince some of my family members that the skink was not "poisonous." There's some old wives tale here in the South that skinks are poisonous, or venomous.