If you are working with the BI Platform, then your best bet for security and permissions help is to read the Platform Administration documentation.
You might also consider contacting Tech Support for more help. Generally speaking, it is probably better to follow a security model where you restrict access to SAS libraries, data and/or stored processes or other content by using SAS Management Console -- instead of restricting access to operating system directories.
You may or may not have access to SAS Management Console and so you might also want to check with the SAS Administrator at your site for more help with this task.
I don't think that File navigation has anything to what kind of metadata credentials each user has. I can't see that the file navigation windows in EG (and DI Studio) interact with SAS metadata. So I think you have to control this at the OS level.