I love your set up, what a nice looking place. I feel your pain when it comes to ducks and mud, they just love it, we let ours roam around and it took care of any mud problem, they seems to be more happy with nice bucket of water and a lot of green grass to roam around, mind you, we have small yard, just a little pizza cut city lot with huge house on it, so there is not a lot of room to be free, but never the less, they do enjoy it much better then enclosure, and it is much cleaner, and the grass is greener, we have not used any kind of fertilizer for years. Summer time we have them in the enclosure but fall and winter they are allowed to be free. Also we took care of duckling problem, I love little ones to run around the yard, but then they grow up to be a messy little creatures that eat and poop, so we send our drakes to the freezing camp.
Yeah, we have 2 malamutes who desperately want to consume the ducks. Being "free" in our back yard is not much of an option for them. The main priority for my build is that I don't have to go out there every day to fuss with them. Leaving for 2-3 days is no biggie as long as they have food and water and are safe, and currently they are.