Three years ago we shut down as soon as the setup was complete figuring the apps would finish later.  Lesson learned, all of the apps got stuck on installing.  So now we do the same as you and always move them somewhere else (distribute around the building to different AP's) to finish their installs before shutting down and collecting again. We do have the delete permission on for students, so they can delete stuck stuff and wait for inventory and they'll come back or they can call us and we can manually do an inventory and get them back sooner (this is how we fixed it three years ago with little intervention). This year it seems we are in the exact same boat with around 1200 iPads between 2 of our buildings.  Because we have so many again with most or all of the apps stuck, we made a static group named "[Building] remove all apps"  and then went to each of the ~15 apps that we have as automatic install and excluded that static group.  Then when we have one or many with stuck apps (listed as "Installing" in Jamf instead of managed), we go to the static group and checkmark the one or multiple, give it 10-20 minutes or go watch a single device for it to go through all of the remove commands, then uncheck them in the static group and it'll reinstall all of the apps.  Not sure what we did to cause it to happen again this year, but if others are running into to it maybe it's not something we caused ourselves.  We did find you do need to wait for the remove commands to go through, otherwise if you have it send install commands too soon it'll just cancel the remove commands since technically it's already "installed".  Other steps we've tried to resolve this on all of them at once without doing an uninstall/install is to uncheck/save/recheck/save the "Assign content purchased in volume" box on one of the commonly stuck apps as well as clicking the force update button on the General page (all of our apps are set to auto update anyways so very little happened with that one).

@mstydel Thanks for your response!

It turns out as we checked in with all our schools, only one his having this issue, and they are also our 

LIGHTSPEED test school... a clue!  Funny that this was not an issue when we rolled out, but looking back in history it turns out that the Lightspeed: Relay Agent (app) installed on those devices  LAST and so all the other apps had already installed.  Don't have a fix yes but ticket open and hopefully soon

Interesting.  We have Relay on all of our student devices and didn't have any issues with our "carted" K-4 devices.  Those stay on and plugged in all summer, though, so they just do app updates and such throughout the summer vs sitting for 4-6 weeks after wipe/setup until given to students and getting turned on.