I'd definitely call this a very low priority task, and maybe is even not worth it if it's very complex to do.
Basically, if a user doesn't mark a notification as read on a wiki and that wiki is subsequently deleted, the user will retain a Meta "residue" of that notification and will be unable to mark it as read afterwards since it says "No sitename set", so therefore will be stuck with unread notifications forever.
The solution for that issue is to delete the entry from echo_unread_wikis, so I was thinking this should be made into an automatic process which is integrated in one of the scripts in charge of deleting wikis/marking wikis as deleted, so that once a wiki is deleted, its entry from that table is removed. So something like DELETE FROM echo_unread_wikis WHERE euw_wiki = 'xwiki';
(See T6509 for the bug that was reported and fix, for reference)