I can't speak for all applications, but you certainly can create hidden applications (i.e. sub-forums) if you have a MIXED application at the top level. (I believe it will work with others application types but haven't tested them personally.)
The process is to remove the "View" permission for the top level application (you could also choose to clear the "Create-topic" and "Reply" permissions as well) AND also to set the option at: Options > Application > Extras & Add-ons > Content > Smart Application Pages. (Do read the caveat on using this option).
You will then need to add back the "View" permission for each and every sub-forum individually (as otherwise they inherit the permissions from the parent application). Obviously, if some applications are to be visible only to those in the "Registered" or "Members" group then you only add the view permissions for those groups for that particular sub-forum. (You'll also want to set the "Create_topic" and "Reply", as required, as well)
The thing that I particularly like about this working with a forum set up in this way is that if someone attempts to post using the "New Topic" option at the top of the forum, they get taken to a screen that invites them to select an appropriate sub-forum for their topic AND only the sub-forums to which they have viewing/posting rights will be displayed on the list.
Volunteer Helper - but recommending that users move off the platform!
Once the admin for GregHelp now deleted.