Well.. how many highly literate and academically educated people believe in horoscopes and astrology (and even if they don't admit it openly they still peek at the horoscope section of the news)?
I don't see this as a huge contradiction.. in fact i don't think Castle believes in these things at all but enjoys the what ifs and the "scaryness" of it all.. he watches Zombie movies with Alexis and reacts in "panic" and fear to events in the movie. It's the same with all horror movies and halloween where people like to be scared and scare others with stories and such even though the rest of the year they are quite logical and "sane".
It's why people watch horror/supernatural movies at all.. entertainment and the fun of getting scared for a time and i believe Castle falls into that category big time (and one of his trademark character bits is that he likes to annoy and tease people for fun, especially Beckett, so that's a tool he has). He just likes to goof around and in that he's been written pretty consistently.