That is correct. The plugin isn’t currently doing anything to handle the deletion of topics that it has published to Discourse. It would be possible to have the plugin configure (or have it ask the site admin to configure) a “Topic is deleted” webhook on Discourse and then use that webhook’s requests to delete the metadata that associates a WordPress post with a Discourse topic.
I don’t mean to answer all your WordPress related questions, but I did a lot of work with the WP Discourse plugin in the past 