Generally I open the notifications and if I’ve to reply I do it from there only. Then I open something else. Notification count doesn’t go away automatically and ‘mark all as read’ has to be clicked. It’d be nice if the notification count disappears after the user open them once.
I think I would like the bell at the top of every page to go away once I click it, but I see the value in not removing items from the actual notification list until an explicit action. However it would be nice if explicit actions like reply cleared items as well.
Personally I get my notifications by email so that bell is just an annoyance. I already have a list of notifications in my inbox.