They're not canon, since they were written by Tomoco Kanemaki and follow the KH novels' continuity (considering half of Aqua's excerpt is a copy-paste from a novel scene). But at the same time, the purpose of the files seem to be solely for providing some insight for the characters, and I'm not sure they cover things that the games moving forward will actually address, so I would consider them free headcanon. You can consider them canon if you want to, but don't be surprised if the games contradict them in the future.
I haven't read most of the character files, so I can't speak much more for them.