Our ducks spend their time in pens when we can't keep an eye on them or they're not in the tub taking a bath. We only diaper them when they are in our living room floor.
All the adult duck pens are at least 14 sq ft per duck (10 sq ft run space and 4 sq ft coop space). We have a couple pens right now (until we build a larger one that will fit all 6 ducks). One was meant to be temporary until we build the bigger pen. It's just a large bookcase we bought from the as-is dept at Ikea for $15. We laid it on it's side then tiled and caulked it to prevent water leaking. We used some 2x4 planks to extend the height to about 5 feet and made walls and a ceiling out of tarp. Total cost was about $60 (half of that was the tiles!).
The other pen was supposed to be a permanent pen when Nettie only had 2 ducks. It's a split level design with a food center on the top floor, an enclosed coop space below that, and a general area at the same level as the coop space. The food center has wire grates for food and water to fall through into plastic bins below. this makes for much easier cleaning.
The new one will be about 20 sq ft per duck. In addition to exercise from being diapered in our living room, we also take them for walks when the weather is reasonable and let them run around to and from the bathroom when they take baths. If we didn't do that, I'd want to give them more pen space.
The pen only needs to be high enough to prevent them from flying out if they can fly a bit. 2 to 2.5 feet seems to be adequate for our runner ducks. I'm guess that's more than enough for a heavier duck (other than muscovies)
For the flooring, we tile it with cheap stick on tiles and seal them with caulk to make it easier to clean (you can wet it when cleaning). Alternatively you could seal a wood floor with polyurethane. This would be a bit too slippery for a duck to walk on directly so you'll need bedding material.
We use wood pellets that expand into sawdust for the bedding. it probably doesn't meet your need for the bedding to be light and relatively dust free. We tend to have dust around the pens so this might not be a good fit for you.
You'll need to balance out the following factors for the bedding:
- absorbent - the drier the bedding stays, the less it'll smell. I find saw dust is a lot better than everything else when it comes to absorbing moisture (splashed water and poop). We mix in a product called Sweet PDZ that also absorbs moisture and ammonia to help reduce odors. It comes as either a fine powder or sand-like pellets (still very dusty when you are moving it around)
- softness - you want it to be soft enough that it won't hurt your ducks' feet. We've had bad luck with shavings cutting one of our duck's foot.
- availability - we have to drive about 20 miles to get our bedding but it works best for us. I could walk down the street to a pet store to get straw...
- cost - we could just line the pen with cut up baby diapers to get really absorbent bedding but that's very cost prohibitive...
- ease of use - having to change the bedding every day or just once in a while with daily touch ups. With saw dust I can scoop out dirty spots daily, turn over or mix up the bedding, and only do a full change every 4-6 weeks. When I used puppy pads for the ducklings' brooders I had to change daily. I could only use puppy pads for a few days before they pooped so frequently I would have to change them multiple times a day.
- messiness - puppy pads are easy to clean up. Just pick them up and put down new ones. Saw dust, shavings, straw, etc require quite a bit more time. I spend about 2 hours per duck pen cleaning them out completely (shovel out the saw dust, bag the trash and throw it in the dumpster, vacuum out what I couldn't shovel, scrub down the walls and floor, disinfect, lay down new bedding, scrubbing and disinfecting food and water bowls, etc.)