VaultWiki 3 and 4 have had 5.4 support for over a year now. It's possible Strict Standards will break in both when vBulletin 4.2.2 is finally released. If that's the case, only VaultWiki 4 will probably be updated, due to the way our release exporter is architected.
As for 5.5 support, only VaultWiki 4 has that. VaultWiki 3 is only fully compatible with PHP 5.5 (no deprecated messages), if all your forum languages are UTF-8 and if auto-links are disabled. If you are going to upgrade to PHP 5.5, you may as well also be upgrading VaultWiki.