Hi,
With hundred of layers, I always group my layers. It was the same in Arcmap but, one think always frustrating me is if a link is missing, you can't see it unless always expand the group and sub group. For now, I have a bug showing missing link but they are there in the map so...
It will be very nice when layers are group with a missing link inside the group to show the mark on the group to make it more easy to pinpoint. Maybe a yellow "!" to indicate a problem in this group.