I use deep litter and it works well.
In the duck house (Little Fort Knox), there is currently about a foot and a half of wood shavings. That gets stirred every day or two, and I add about one part peat moss to ten parts shavings to keep the pH elevated enough to discourage ammonia from forming, as it sometimes does in humid New England. The floor of the duck house is linoleum, which goes up the walls several inches and has a 1"x3" furring strip across the top to keep poop from getting under the linoleum.
I put a few inches of straw on top for the ducks to nustle into, and to make nests with. I pull the straw out every few days and put it on the garden or compost.
The veranda, an attached porch, has a half inch hardware cloth bottom with an inch or two of sand on top. I use sawdust pellets there, since that is where the water and food are (not in the house). I use a cultivator to fluff that sawdust, and it smells good and earthy. After a week or two (depending on weather), I dig that out, compost it or mulch with it, and replace sawdust pellets.
The Day Pen also has a relatively deep litter bottom. The pen itself has coated chain link underneath for security. On top of that I have been using straw, and sometimes some coir or dry leaves. Over the last couple of years, all that has broken down quite nicely, so there is a cushy, composting material. Worms come into that, giving the ducks something to forage for. I occasionally turn it (with the ducks right there with me), and sometimes I pull some out for gardening. I toss fresh straw in there occasionally, too.
It took a few months at least for the composting process to really get started but now that it has, the system seems to stay in a nice balance and I have worms for the ducks, more compost, and less maintenance than I did at first.