Many types of notification will neither update or even let you properly mark them as read. For example if one were to recieve an e-mail through the English Wikipedia — and be notified on meta, it is neither possible to mark it as read, nor does seeing it on meta mark it as read on en-wiki. On the wiki where the notification originated it is possible to mark it as read, but this does not move to other wikis, for example when going to sv-wiki after this it will still appear as unread and red, despite having seen it several times and multiple tries to mark it as read on sv-wiki. Sometimes after having been able to get rid of it, the same notification will appear again.
After an arbitrary time the notification however dies down and stops appearing all the time. This seems to only apply to certain types of notifications such as e-mails (and some others I can't think of at the top of my head).
It would be preferable that once a notification is marked read on one project that it is marked read on all projects — and that functionality is the same for all types of notifications.
Edit: Switching to the mobile viewer at for example en.m.wikipedia.org also brings back old already seen mail notifications. Does not revive other types though.