Combining the Same Terms in different Vocabulary as one
You should try putting both Category and Tags under a single master vocabulary. Then assign both Category and Tags as parents of the shared term. So you have:


Level 1: MasterVocabulary
Level 2: Category [parent:MasterVocabulary], Tags [parent:MasterVocabulary]
Level 3: SharedTermA [parents:Category, Tags], TermB [parent:Category], ...