I have found out what the problem was. It seems to be an issue in the ionic-platform-web-client.
In the generated code in the ionic.io.bundle.min.js file there is:
e.pluginConfig.android.senderID=t.app.gcmKey
so when I run the app, always the GCM-Key is in there. Now to test I have set the senderID in this file manually and now it works.
Seems like the ID is not loaded from the package.json.