At the moment it is not possible to use the "_hidden" tag in filesystems other than layer.xml.

Example:
Provide following filesystem to the system filesystem via META-INF/services/org.openide.filesystems.FileSystem

public class LoginFileSystem extends MultiFileSystem {
    public LoginFileSystem() {
        try {
            FileSystem memfs = FileUtil.createMemoryFileSystem();
           	memfs.getRoot().createFolder("Menu").createFolder("File_hidden");
            this.setDelegates(memfs);
            System.out.println("Debugging message");
        } catch (IOException ex) {
            Exceptions.printStackTrace(ex);
        }
    }
}

This doesn't hide the file menu, but for consistency of filesystems it should (filesystem in layer.xml and user
directory do hide it).