Board Thread:General Discussion/@comment-452-20130418224345/@comment-5887706-20130418224818/@comment-452-20130425062225

I was pleased to discover that Wikia have now fixed this problem.

When highlighted threads are deleted, notifications are now removed, whether or not they've already been seen or clicked on.

So I guess that Wikia concurs that there are no genuine uses for keeping a notification for a deleted thread.