Is the GarageBand app automatically deployed to the student device, or as a self service download?

GarageBand is automatically deployed to all iPads. On the iPads I tested the GarageBand app is working and on the latest version, as is the teacher's iPad. 

When starting a Lesson where the GarageBand app is allowed, it just vanishes off the student's iPad, and can neither be run by searching for the app. 

Just tried replicating your approach and the apps are all showing on my device.  Let me dig in a little to see what I can find out 

The apps I tested so far are:

Working: All MS Apps, Doodle Spell, PicCollage, Stop Motion, LynxWhiteboard.

Not appearing: GarageBand, Doodle Maths/Times Table/Spelling.

We do use the Layout function to group the app on the iPads, but iMovie and GarageBand are in the same Layout folder, yet only iMovie appears when the Lesson starts

When you deploy the Lesson, does it take the apps out of the folders? 

Yes, the GarageBand and Doodle icons are removed from their respective Create and Doodle folders.

And every time the Lesson ends the Web Clips from the Websites folder are multiplied onto the Home screen, so we now have multiple copies from the Web Clips folder filling up the Home screen.

I created a brand-new profile and freshly reloaded some iPads to test the Teacher app function again. Unfortunately some apps still do not show, yet the same apps show perfectly when using Apple Classroom. Also the Web Clips just keep multiplying on the homescreen. I have now completely removed 2 of the Web Clips from the Profile but the icons still remain on the Homescreen, albeit without the picture icon I previously uploaded for them. 

If anyone has any suggestions on how to get the Jamf Teacher app and Web clips properly working please do let me know as we have now run out of ideas or work arounds.