Answering my own question in case others stumble upon the same problem. On my StageWebView I had a listener:
htmlContainer.addEventListener(LocationChangeEvent.LOCATION_CHANGING, handleExternalUrl );
My problem was twofold. Firstly, I had to check that the .location property on the event-object passed to my handleExternalUrl-handler did not contain the string "apollo.air". No url should ever contain a TLD called .air so this test will never fail :-)
Secondly, I was calling .preventDefault() and this prevented other things to happen as it should in the app. Now works perfectly. It's still odd that this only occured on the iOS devices and not in the iOS simulator or any other devices.