Let me post menu.module suggestion. Let's say that is defined a vocabulary containing many terms. The terms may be assigned to an article but many of them not assigned, they are ofphans. In 4.5 Drupal we genarate menu tree based on the vocabulary. Menu will consist of many item linking to empty page. It's possible to enable or disable item manually but when someone assigns article to the corresponding taxonomy item it should toggle it.

I think that "auto enable/disable" feature could help. Enabled menu items could be visible only if are no empty (of course attention for tree structure). Such checking probably takes a lot of time but implementing using menu_cron hook should be effective.

Tomas