Walking in the pond will relate pretty quickly the depth of the layer of organic material on the pond bottom. Your feet will sink into a layer of black ooze. I'm guessing your pond likely has 12"+ layer. I have used both excavator and dozer on ponds at my place, depending on the nature of the pond bottom. Too much material and a dozer will get stuck, need long reach boom on excavator to remove in that case. I think it's a good idea to excavate if you are draining, get a new lease on life of the pond. If you do so, I would bet the duckweed would not find establishment easy with removal of nutrients. Clean slate for you, blank canvas.