Well....it was sorta answered with
If a stranger owns the other side of the fence, it is to easy for things to go wrong. A dog frantic to enter the coop is a good example. Also, neighbors might complain that the chickens are too close to them.
However, in your case, since you own both...
Muscovy ducks have long nails, and will dig in the dirt at times.
So yes, I think a hardware cloth floor would cause foot sores and could also snag a nail.
So..... a hardware cloth floor isn't a good idea with Muscovy ducks.