Here’s a final update, after lots of further testing and in-depth contact with UM support:
ad 1) The irregular behaviour of restricted menu items can be resolved by disabling or removing the WP User Frontend plugin, or by installing the WPFront User Role Editor plugin. The latter has a setting which allows you to disable menu item restrictions by WPUF.
ad 2) The incomplete member directories were caused by imported users. The missing users were all imported into WordPress with Ultimate CSV importer, and apparently imported users are only shown to admins by UM until they are ‘Reactivated’. You can do this from the Users overview in the backend > select relevant users > click on UM Action dropdown > select Reactivate). I have asked UM support to include this in their documentation, in case other people use an importer to bulk create new users.
ad 3) If UM restricted taxonomies do not work properly, the cause may be the ‘Hide from queries’ setting that can be activated on a taxonomy term (um_content_restriction__um_access_hide_from_queries). If multiple taxonomy terms apply to a given content item, and each term has different role restrictions with ‘Hide from queries’ ticked, a user that does not have each applicable role, is not able to see that item.
For example, if a post has taxonomy terms ‘Group A’, ‘Group B’ and ‘Group C’, and access to ‘Group A’ is restricted to ‘Role 1’, ‘Group B’ is restricted to ‘Role 2’ and ‘Group C’ is restricted to ‘Role 3’, a user with just Role 3 can not see the item.
Unfortunately, it is not possible to simply untick ‘Hide from queries’ for each taxonomy term, because in that case, user with Role 3 will also see posts that should not be accessible by him/her. That is, in search queries, archives and single posts only the main contents is hidden, while the title and featured image of a restricted post are still visible.
To resolve this issue, I have asked UM whether it would be possible to adjust the ‘Hide from queries’ parameter, so that it checks whether a user has ANY role that may view / access the contents, rather than ALL roles. They indicated that this is beyond the scope of their support, as they already offer a’native’ way of restricting access rights (which works well). So my conclusion is that if you have multiple groups / roles that should have fine grained access rights, you should stick to the ‘native’ UM way of restricting access (even though that does not (yet) allow for bulk editing), or find some other tool that does the job as well across all (custom) post types. Do not use taxonomy terms with role restrictions set by UM for that.