I use pet carriers : the ones with top and front doors are best. I have one size that takes a pekin sitting down and a larger size that takes a muscovy drake sitting down. Most dogcrates are too large for transporting ducks as the duck can stand up and move around, which is not safe. I have used a medium dog crate with front and side doors, with a divider, for 2 muscovy drakes. They sit sideways and although they have the headroom to stand up they are too confined in space to move around. When I had a tightly bonded pair of pekin drakes I could transport them in one medium dogcrate without a divider. I have also used a large heavy duty cardboard box: it had originally held a printer. It was a good size and with holes drilled round for air proved a good emergency carrier.
When I can plan a trip rather than going and picking a duck up in an emergency, I restrict their access to food ( but not water) for a couple of hours before travel. I offer them Pedialyte or Liquid IV solution every hour while traveling. They always sit on a puppy pad in their carrier, crate or box. Two of my current flock have traveled long distance with me several times with no ill effects.