The FPolicy settings configured by the agent on NetApp will remain until the Managed Host is deleted. These settings will have no impact on the NetApp if the agents are no longer registered.
If the options above are not enabled when the agent is deployed, then no FPolicy will be set, because it would not be required.
Enhancement ID 448804 has been submitted to provide an option to either remove these FPolicy settings automatically, or provide a way for them to be easily removed if they are not required. This will be reviewed by product management and considered for possible inclusion in a future version of Data Governance Edition. No ETA is available at this time.