When you visit the plone site (http://plone.org) you see that the side navigation bar (viewable at any page besides homepage) contains only the root folders, the item and its immediate ancestors. A very nice behaviour, and one I spent a while fiddling with navigation properties trying to make happen.
But actually the solution is much simpler. Every version of Plone since 2.1 comes packaged with two identical states ‘public draft’ and ‘published’ – items in either of these two states are available to the general public. Why two identical states? Well, it does enable the user to choose which items he wants public but not available in navigation by putting the items he wants available in navigation ‘published’ and the ones he doesn’t ‘public draft’, say. Then he can go to navigation properties in preferences, check filter workflow states, and put in published into the box below.
That’s what Plone have done on their site: in addition, only the folders at site root are published, and all other content is visible, so that it will only appear in navigation if the actual page is selected.