I allow my 5th grade up crowd access to both series (39 Clues AND Percy Jackson).
I have to explain that we do ALOT of discussion with our books and the kids are TAUGHT to analyze what they read. That being said, the middle school crowd are not the most analytical people I've ever met and they ususally need help.
The gods in Percy Jackson, who do bad things, are presented as good people and the kids need help to see that their bad acts, no matter how funny & likable, makes them bad characters. The kids DO NOT see this on their own and argue vehemently that because they are likable, the gods are good characters.
In 39 Clues the main characters (children) must do morally objectionable things (steal boats, even if it's from bad guys, tell lies) and it's all presented as very justifiable. My kids need talked through each moral dilemma - they won't necessarily see that the kids in the story have a choice to do moral actions when the immoral actions are presented as so reasonable.
As long as you talk through the issues in the books with the kids I see them as positive learning tools. (Which is NOT how I see those vampire books...) Yes, the books are mainly for enjoyment and can ABSOLUTELY get a struggling reader (even an older one) hooked on reading. But I completely agree with Martin Cothran - "Literature is dangerous—except when taken in large doses." http://www.memoriapress.com/articles/harry-potter-and-attack-critics The above series' are books my kids read during summer or a break from school. Their minds are FILLED with historical characters or classic literature the majority of the year. I feel like that helps protect them from the "twaddle".