TheBoost said: The reason is plainly because Anakin refused his roll as Chosen One when he met the three ghost god things on planet Mortis and didn't bring balance to the Force somehow.
The Vong books were published in 1999-2003. Mortis first appeared in The Clone Wars in an episode aired in 2011 and was tied to the post-ROTJ state of the galaxy in a book published in 2012. In short, the link between Mortis and the Vong is a retcon that was created 10 years after the fact.