So just a comment on a couple of things and then my set up.
I wouldn't use hay at all. Hay will mold really quickly. Stick to straw or shavings. Less mold growth with those two.
Secondly, that goat trough you have, I tried one just like it when I had my ducks about 4 years ago and I almost had a duck drown because he squeezed his fat butt in between the wire guard and then got stuck and couldn't get out then got waterlogged and exhausted and cold. Thankfully I found him in time, he must have been there for hours before I got home, and I was able to dry him off with the hair dryer and revive him but since then I won't use those water troughs for ducks. I bought a 125 gallon water trough and built a ramp up to it so they can get in and out of the water to clean off and then I drain it into my garden or holding tank for my garden. I clean it out about every 2 days in the summer because they can make a mess. Right now I have the front opening rubber maid containers with the 5 quart feed pan inside and a milk jug gravity waterer inside to keep the ducks from climbing in the pan.
Right now my new flock is only 4 weeks old going on 5 weeks and they make a hell of a mess. I clean their "pen" every day because of the mess they make and I only have 11 ducks.
As for the bedding, my duck run is a dog run, 32 feet by 6 feet, wood fencing on the long sides and then the dog kennel panels at each end. I have hardware cloth from the ground up to about 3 feet on the panels because I've had a raccoon problem in the past. I used welded wire fencing across the top to keep out the winged predators and the racoons. The pen is 7 feet tall. Since I don't live in an area with extreme weather I don't actually have a full house for the ducks. They have a lean to area in the back with plastic greenhouse panels over the top to keep off the rain. I have a 6'X8' "deck" made of pallets that I cover with straw and There's a extra large dog gloo up on the deck. I have home depot buckets modified to lie flat on the decking that are used for nesting boxes. I put straw in those as well. The rest of the pen is covered in wood chips and then I have a plastic dog deck right in front of the door to cut down on the mud and tracking at the entrance of the coop. During the day the ducks free range either in my yard or across the street in my garden. I have portable fencing panels I use to keep them penned in the area I want them to patrol.
I also bought some cameras off of
Amazon that I've installed in the duck run and across the street so I can monitor what the ducks are doing. I plan on getting them for other areas as well. They have a wireless capability so I can stream the feed at work and keep tabs on them when I'm not home.