Well the severe issue is fixed
https://github.com/discourse/discourse/commit/67f404d281b7dbd5867fe5332968f7855ffa4e9c
If a PM or topic is deleted its now yanked out of the notifications stream.
There is an edge case that still needs to be fixed but is harder. If a topic is moved from a category you have visibility to one you do not, we are not yanking out the items out of your notification stream.
Will leave this open till I fix that.