Hello there!
The Active Directory Domain Scanning target will enumerate and query all available domain controllers to retrieve a list of computers and scans those computers. By default, this will indeed cover the entire domain.
So if your Lsagent-only computers are in distinct OUs, it would make sense not to scan these (for multiple reasons) and use an OU filter to weed out those assets from your agentless scanning targets.
This will result in the Last on-premises AD Domain date no longer being updated for these Lsagent-only computers, and if this date was preventing the cleanup option from kicking off, resolve your issue.
Don't worry about not getting any AD information for your LsAgent-only assets. While LsAgent in itself cannot perform an AD Lookup, an AD Lookup will be triggered after an LsAgent scan. For this to succeed, your scanning server does require a credential mapping to the correct AD domain with a credential that can read your AD.