Why can I not see certain categories in the Navigation Structure despite supposedly having access according to the category settings?
If a category does not contain any documents (i.e., is empty), it is hidden from users in the navigation structure until it contains documents. This means that once a document is published, the category and its documents will be displayed.
Note that this does not mean the user cannot publish documents in a category that is not visible in the navigation structure. The category will appear in the publishing dialog, provided the user has access to the category, of course.
Note: This does not apply to users who, through their profile settings, can manage All categories or those who are Category Managers, as they have extended access and can view categories without documents. This is to allow the user to manage category settings even if they lack documents.