Seems the mystery was solved: The beeping seems to be caused by brltty. The init.d script reads /etc/default/brltty which has "RUN_BRLTTY=no", so we never actually run this by default. But the systemd unit does start it. Apparently brltty produces the beeps as a kind of notification to blind users, so it sounds plausible that this is deliberate.
So I think what we should do here is to make the systemd unit respect the default file.
Seems the mystery was solved: The beeping seems to be caused by brltty. The init.d script reads /etc/default/brltty which has "RUN_BRLTTY=no", so we never actually run this by default. But the systemd unit does start it. Apparently brltty produces the beeps as a kind of notification to blind users, so it sounds plausible that this is deliberate.
So I think what we should do here is to make the systemd unit respect the default file.