Libraries will not be shown in Enterprise Guide if they are preassigned and then fail to assign. In SAS Management Console right click the library and select "Display Libname Statement" and then try to run that statement in Enterprise Guide and see if it produces an error.
For Files, your user Id may not have permission to list the contents of the root path defined. Check the current setting for the path and see if your user Id has permission to list the contents. If not it may need to change.
Usage Note 59828: Setting the file navigation path for a workspace server
https://support.sas.com/kb/59/828.html
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Greg Wootton | Principal Systems Technical Support Engineer