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Just raise a maintenance advantage support ticket (ma.commvault.com or call them).
That is true. Unlike VSA where you can ignore empty subclients, there is no such Additional Setting for SQL. A hack to get around this is putting a System Database in one of the subclients, but I would recommend raising a Customer Modification Request via Commvault Support to get this feature added.
The Schedule is smart enough to skip Transaction Logs for Simple Recovery Model in a subclient, you will however need to manually separate the databases into another subclient if you need different intervals. Also, make sure that you either set up the subclients that support auto-discover for new databases, or if you you want only protect chosen ...