In what context should it hide the topic. By default it hides inaccessible pages in actions like page index or backlinks. The config parameter responsible for this is hide_locked. You can find the setting in the Admin panel under Preferences -> Permissions -> Miscellaneous. Do you have an example where it should hide the link, but it doesn't?

This behavior does not apply to links you set directly inside a page like ((ProtectedPage Hide me)).

My bad, I was meaning the Homepage or just any page in general.

It is technically possible to add an option to the WackoFormatter to hide links like ((ProtectedPage Hide me)) to inaccessible pages, but this is conceptually not desired. Using the tree action or a customized action for this purpose is probably the best way.

There are a couple of possibilities to show only the pages the user/usergroup is allowed to access.
The following solution is the easiest and most common one.

HomePage:
{{tree page="/Manual" depth=1 title=1 nomark=1}}

1. The Manual cluster ensures, that it loads only the pages inside the cluster.
2. The depth defines that it shows only the first level.
3. The nomark parameter suppresses the frame around the results.
4. The title parameter ensures it takes the page title (default).

Of course it depends on how you want to organize your wiki structure.
Usually you set a GROUP in the read ACL's and add than the users to that group.

You may copy the tree action and create a modified version which fits your special purpose.
For some reasons there is no template for the tree action yet, where you can change the output directly.