The stories are canon. If the games do not contradict them otherwise, anything Kanemaki writes can be considered a form of canon information as Nomura provides her with supplemental information about the games to add into the novels and oversees their creation.
The novels thus far have been home for revealing that heartless and nobodies once both killed can be returned as a full human (KH2 novels), that Axel was coming back to life (KH2 novels), that Vanitas remembers the UX past unlike Ven (KH3 novels), and a ton of other information.