I've hatched relatively small clutches under multiple ducks/chickens. They do steal eggs from each other a lot, but it hasn't been a problem in my experience.
They won't notice if you take some of the eggs. My ducks can tell the difference between "many eggs" and "no eggs," but not between "many eggs" and "some eggs." But you could play it safe and take, say, ten today, ten tomorrow, and so on until you get to six or whatever number you choose to hatch.
If you have any other ducks laying, I'd recommend marking the eggs you want to hatch with a permanent pen to be sure they don't keep adding new eggs to the ones that are already incubating.