Initial answer on SharePoint designer checkbox is very helpful. To the comment about the feature hiding the element from "Site Content" as well - there is an easy work-around for that. Just build a Site Admin Link List and make sure to create links for all hidden elements before hiding them. Then set security on link list to just the people who need access to the hidden elements. This provides way for site admins to get to the hidden elements when needed but allows you to follow instructions in this topic for hiding it from tree-view and navigation.
Note too - it is only hidden when you are on a standard site page. From LSB, click the "Libraries" link or "Lists" link and when you jump to that page and scroll to bottom you should see the "Site Content" link re-appear in that context. (at least it did for me). I believe we are using SharePoint 2010.
Untested: I also suspect you can add a link on navigation for the site (to appear in global heading, or LSB) if you need to and this could allow you to link to a desired feature in navigation while hiding it from treeview (but i haven't tested this idea yet).