That is an interesting question. In the case of the Da Vinci Code, it would say it comes down to the way the author crafts a storyline around all those elements (all the different clues, iambic poems). I guess that could be perceived as cleverly done if it wasn't for the fact that the central theory in the book is not in fact his (coined for the first time in a similar book in the 80s*) or for the fact that most of his interpretations are false and that there is no real basis for any of his conclusions. It could also be because you have to think when you read the book. I don't think it is an intelligent book, though.

I think it is inevitable that any book with a message and enough art and history references will be seen as intelligent by society in general. A little bit of intelligence by association, I guess.

Is Pratchett's work intelligent and why would it be? The knowledge, the references, the message? Frankly, I don't know. I think it is, because of the detail and the depth, but for a large part it depends on your perception and definition of intelligence.

Edit: crosspost

*Pretty popular book, so this wasn't even the first time this theory was presented to the public.