I got fed up of idiots in one of my groups and changed their killfile entries from "mark read" to "deleted". Much less traffic, hurray! But it reveals that Usenapp isn't very good at threading around missing/deleted messages. Replies to deletions get set to the zero-indent level of the thread tree. I guess it's using In-Reply-To: for the structure?
Very much a nice-to-have/nonessential/backlog item, but it can be fixed as in most cases there's the References: header as well as the In-reply-to: header, so the threading could be reconstructed despite the gaps.