We actually have a "mark as read" button. If you hover on a notification, there is a little tick symbol on the right side that you can click on to mark the notification as read.
There are also "mark all as read" and "delete all notifications" buttons in the top-right corner of the notification box.
Unfortunately there is no way to delete only a single notification. That's just a limitation of Flarum's notification system.
Hope this helps!