Look at function build_notifications() in file includes/class_bootstrap.php. It looks like you could have a plugin using hook location notifications_list and modify the $notifications[] array. I can't remember offhand how it works, but I believe if you add a notification, there should be a value added to $vbulletin->userinfo[] with current the number of notifications.
Edit: squidsk posted while I was writing, but anyway, I thought I once knew how to do it.
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