Database helper is designed to give additional methods for developers to access the database, including adding foreign keys.  Database helper also improves the security by making any calls that go through $db->helper require using the drop_table, truncate_table, and delete_query methods or they will not execute.  It also logs any query that takes longer than 2 seconds to execute as long as it was called with $db->helper.  The log can be viewed in the Admin Control Panel under Tools & Maintenance.  Full details can be found on Github.