I think this is most likely a Drush issue not warning you about deleted configs.
I believe the core Drupal UI should warn you about configs that will be deleted/modified as part of an uninstall if they've been added as a dependency.
- Status changed to Closed: duplicate
almost 2 years ago 1:23pm 15 March 2023 Seems like a duplicate of 💬 Uninstalling Context module, deletes blocks configuration Fixed