Eddie,
I think islands like you describe in the deep areas of your pond are really a big plus to fish habitat. We build underwater "islands" in the deep areas of our ponds in an attempt to make use of what can otherwise be basically unused water below the thermocline. We build the islands with a base of materials from the pond bottom and then add permanent structure to that base taking it to within a couple of feet below the surface. They are fish magnets in our ponds and often preferred even over shallow water structure. Both LMB and HSB use them and the largest BG ever caught from our largest pond came from one such island. Leaving it a couple of feet or so under water prevents snakes, birds, animals, etc. from making use of it and also adds to the fish use of it. I recommend them.
