Since the admin links pointing to these options all disappear after the add-on is disabled, I'm assuming that the admin page containing the link had been loaded in another browser window prior to disabling the add-on.
This will be fixed in the next release. The bug had existed in all prior versions. Now, if the add-on is disabled and the link is known or accessed directly, admin options that had special rendering will not be rendered at all (missing from the list). Also, in this scenario, beware that when saving most VaultWiki options that are rendered, the new value will be accepted without checking for problems or causing rebuilds; this may result in problems after VaultWiki is enabled again, requiring manual changes/rebuilds, but would not be considered a bug.