I think i have found the issue causing this, as it happened to my school recently due to creating an intranet page for students/staff
Problem lies in setting the default homepage through group policy for internet explorer, at first i was extremely confused why all users could see hidden files and folders then i worked out what was causing it to begin with, all users have logged into their workstations at least once since the change so i reverted back to unconfigured logged into a workstation as a student and hey presto no hidden files and folders, dont ask me why this causes it as i haven't the foggiest but im glad i worked it out haha