Is this mud pond going to be used to breed koi, or just as your koi pond. If you are going to be breeding, then the pond will need to be drained to catch the koi, and the rocks will interfere with catching the koi as they grow for culling, selling, or whatever. A friend, who has since passed, used to have his mud pond harvests in the fall, and he would just walk down into the water after it was pumped down to a foot or so and just reach in and pull the fish out by hand with little help from another friend with the net to get the fish to come out of one deep area to the one he was standing in and doing the catching. As long as the deep area that you will be trying to net them from is mud bottom, that is all that is needed. The fish can use the rocks for cover the rest of the year.
Zone 7 A/B
Keep your words sweet. You never know when you may have to eat them.
Richard