I'm the author of the "category levels" plugin, which sets privacy levels for categories. It currently can hide unauthorized posts and categories. The latter is accomplished with the new list_cats_exclusions filter. (Thanks!)
My request is for a similar filter to be added to the get_archives function. That way I can be sure that the count reflects the number of posts that are actually visible to the user, instead of the total.
Here is my plugin for reference: