SmartDL stores the query information in the extensionData attribute of Active Directory. That is the only change. Even if you unistall SmartDlL, the query stays. It is harmless information though. You can use ldifde to clear the extensionData attribute of all groups after uninstalling if you want to keep the directory clean.
The schema files are for external directories (Lotus Notes, Sunone, etc.). They are unecessary though as SmartDL autodetects the schema of these directories. They are provided for users already familiar with the attributes names from previous versions of SmartDL.
--Robert