Since cross-content-type tags are supported in vBulletin 4, we can simply duplicate the entries from the old threads for the wiki content-type. For vBulletin 3, thread tags are only for threads, so without reinventing the wheel, we can store the old tags in a dormant table so they are at least not lost. If the forum is upgraded to a vB4 or 5 which supports tags in other content types, they would become available again. If the wiki is imported to another forum that supports tags natively, likewise this table would be imported properly; otherwise the dormant data would be imported.
Maybe in a few releases we can focus on creating a tagging solution for forums that don't have one in the core software. For now the focus should at least be preventing the data loss of existing tags before VaultWiki 3 and 4.