Using "what" alone is usually asking for a more specific answer. For example: What classes are you taking? Answer: I'm taking Calculus, Physics, Astronomy, and a few others.
Using "what kind of" is asking about a general type. For example: What kind of classes are you taking? Answer: I'm taking mostly math and science classes.
So for your example, if you want to know the types of books he reads, you would say "What kind of books does he read?"
Sometimes, however, the phrases can be used interchangeably.