Per @TheDJ's comment in IRC (refactored),
one of my biggest concens right now is spam... About 9/30 notifications in my mw.org list is spam from the hovercards talk page...
which is a lot of noise for 1 page out of the dozens that i'm watching.
[...] i'm asking for a way - for stuff that gets deleted - to be removed from my list of notifications.
The fix should be: don't delete the notification, just keep it from rendering, so it can reappear if it gets unhidden or undeleted.
@Jaredzimmerman-WMF suggested only removing it if it's unread (T94942: When post/reply is hidden deleted (or otherwise inaccessible) echo notification for the inaccessible content should be removed if unread); however, that could be problematic, since if they click the read notification, it will still be missing, and they might not have access to see the topic title (e.g. if it was suppressed).