turns out, i have installed MR once without the App module.
Then i enabled it on the server and wanted to add the clients without the module.
That works fine until these Macs perform a reboot.
I have done these steps to uninstall MR on the clients:
sudo rm -r /usr/local/munkireport/
sudo rm /usr/local/munki/postflight
sudo rm /usr/local/munki/report_broken_client
sudo rm /Library/Preferences/MunkiReport.plist
sudo rm -r /Library/MunkiReport
sudo rm /Library/LaunchDaemons/com.github.munkireport.runner.plist
sudo pkgutil --forget com.github.munkireport
and reinstalled them with the App module enabled.
Still no Luck, after a reboot they show "0" Apps