right now it is intentionally designed to work the way you described it, i.e. deleted tables won’t be removed for good from the database schema, but instead are only marked as deleted. This is to allow later restoring of a table marked as deleted. If the approach mentioned by Jan-Niklas seems unfitting for your purposes, you could create a feature request in our Ideas portal and let us know about the desired behaviour from your side when deleting tables from a schema created in the Database Designer.
