While sometimes there can be some helpful information in replies to deleted posts or comments, the vast, vast majority of those kinds of threads are just flamewars and arguing

This really depends on the subreddit/community

Some people like to delete their comments for privacy, because they want to move instances, etc. It doesn’t make sense to have that remove entire chains of comments with it. I also don’t think people intend for that to happen when deleting comments.

Mods should have a “nuke thread” button to autoremove all child comments when there’s a mess like you said. Users shouldn’t have that ability, even if they intended for that in the first place