In my experience this is normal behavior. The apps are not just "hidden". When they restrictions are removed, all the apps come back in a random order on the screen. Most of our students have given up on placing their apps in folders, because their teacher's restrictions will place them back on the home screen in a random order. 

Bonus weirdness: We use webclips, and when a teacher's restrictions are removed, our webclips duplicate themselves. The solution? reboot the device or reset the home screen in settings. 

Liminality is right, this is a normal behavior. Because of security reasons Apple doesn't save/share the icon information and so its always a complete mess. Even complete blank homescreens are possible. A workarround is, when you just stick to one single app then it stays as it is. We discoverd this when using only a Dictionary or Goodnotes like in single app mode. The second you add a second app the apps get scattered arround.

Real solution... tell the students to just deal with it. Searching apps is most of the time faster than swiping arround.

Okay, thank you for sharing your experiences. I hope, Apple knows this fact and is working on it.