I agree entirely with wifezilla. Our runner is a little over a foot tall, but you'll need access to clean, harvest eggs and grab ducks, so plan for at least 3 feet high so you can crouch down and sit on your knees if you need to.
when my hatchery (non show) runners stand up at their tallest they are 22 inches tall. but they can "duck" (haha) down to 14in no problem. i have a small nest box in their main pen for them that's 2ftx4ft and it's 18 inches high, with the door to get in to the box about 16 inches high. they have no problem getting in there. I also have a plastic pet carrier i put them in that's 16 inches high they go in when traveling. They can't stand up straight, but they sit in it nicely. If your coop is going to be big enough for many ducks and they will be spending a good amount of time in there, go ahead and make it as tall as you so you can clean it easily. MY nest box has little doors and i have to get down on the floor and use a brush/dust pan to clean it... noooooo fun. but it's only 8sqft. I can't imagine having to do that for anything bigger.
edit: oh and my ducks live inside... so when i'm on the floor, i'm inside where the temp stays the same... i def would not want to be sitting on the snowy/wet/muddy/dirty ground outside to bend to get into a short coop....
if you are building a little hut for your ducks to retreat to, it doesn't need to be tall, but i suggest you make the roof on hinges so you can open it to clean it easily... here's my ducks outside hut-
the roof is only attached to the hut by hinges on one side, so it flips open for easy cleaning