I've been lucky enough to do the Keys bonefish trip a couple of times, what an awesome fishery. I saw fish mudding almost every afternoon/evening over at that public access (Annie's?) on Matecumbe. Never caught one from that spot, but boy were they kicking up some silt! I did get one on the hard shoal just to the right though.
It seemed when they were in the mud there was nothing on the flat. I see you do not prefer to fish them in the mud but what is the best method for these fish in the event that it's one's only choice sometimes?