ok, scratch that it is working… 
As I tried with a different browser (which had never called raspberrypi.mydomain.example.com/nc/.well-known/caldav before) I suddenly got redirected to the correct url https://raspberrypi.mydomain.example.com/nc/remote.php/dav/.
I guess that my first tests with a non working redirection were cached in the other browser and never got refreshed/altered afterwards?
However the configcheck under the settings/admin/overview is still complaining that “/.well-known/caldav” and “/.well-known/carddav” could not be resolved. 
Is the configcheck only scanning the apache config for the redirections?