Installing my click using 'pkcon...' generates a different profile file then when done manually (aa-clicktool & aa-easyprof see https://wiki.ubuntu.com/SecurityTeam/Specifications/ApplicationConfinement/Manifest). The manual way adds extra rules that allow the app to use the media-hub.
I noticed that uninstalling the app did not remove the profile. Manually removing the profile (from /var/lib/apparmor/profiles and from /var/cache/apparmor/) and then reinstalling the click resulted in a profile that could actually work.
After loading it (apparmor_parser -r) my app works!
So I think that after adding the policies in the IDE and installing the new click the previous profile (without the policies) was still being used. Question is why? Maybe because the profiles are cached and I did not increase the version number of my app.