I have every subcategory Obtained under Characters, but the Characters main category does not show Obtained. Why? Are there more NPCs in the game files from areas that aren't even in the game yet?

One way for that to happen is if there is another category for which you are missing all entries.  An empty category will not appear. But it does look like you have them all.

However, bdolytics.com's knowledge tracker shows some additonal categories.  Some are empty, some only have one entry under them, not sure if any are obtainable.  Yet?