However, until I do one of those things, I have the (1) indicator. IMO we should differentiate between new notifications and unread notification, much like we already do for PM's. That way, when I open the notification drop down, it was could send an AJAX request that would mark the notification as seen (ie no longer new) so the notification count would decrease, but it would still appear as unread in the list as it currently does until I actually click on it.
As I mentioned, this is how PM's work, and I think it should be similar for notifications.