is there a way to know how long the data governance agent takes to scan a folder in a fileserver?
Is there a log?
Did you choose only certain folders to narrow down the search field? If you go under Data Governance > Managed hosts within Manager and right click on the agent in question you can get all of the logs for that agent to download. You could also check the Data Governance Edition Service log which will be hosted on the DGE service host in the following location:
C:\Program Files\One Identity\One Identity Manager Data Governance Edition\Server
Look for the DataGovernanceEdition.Service.exe.dlog