To all who have the same problem, take a look at the deployed kdepim-runtime package.
On my system the "akonadi_kolab_resource" was missing. This binary provides the akonadi connector. For some reason my kdepim-runtime package didn't contain the binary. With an upgrade to the developer-version the akonadi_kolab_resource appears again and all works well.
I have a Kolab Now account (I'm assuming it uses the same code base as the community version) and I'm using the Mail client on macOS. It still shows the special folders (Contacts, Calendar, Tasks, Files, Configuration) those are not being filtered for this client.