The vBulletin notification bar gets completely replaced by vBNotifications' bottom left display, the only reason why there's an inbox link up top and not an empty space is because I personally hounded the original developer to include a link to the Inbox as a quick way of accessing it if there were no unread PMs.
The purpose of it isn't to indicate whether there's any unread PMs, it's simply a way to quickly access the inbox when there's no active Unread PMs notifications.