I have never trusted the digital keys, so no loss there.
I received upgrades in advance at two hotels in/near AMS in the last couple of weeks. One was preannounced via email, the other I saw when I went to check in. I have never seen upgrades granted at the time of online check in. If I haven't been upgraded in advance I just ask at the desk.
Interesting info on not all available rooms being loaded for online check in. Here again, if I don't see anything I like in advance I don't complete the check in and just ask at the desk. I always put a "high floor and away from elevator" note in the requests.
I guess I just have set my expectations for the app appropriately. It does a decent job of booking new rooms, managing bookings, and managing the HH account. In the world of travel apps, that's above average.