It really depends on how much time they will be in the pen vs free ranging. A night pen obviously doesnt need to be very big in comparison to a pen that they would be living in 24/7.
What are your intensions for the pen??? 3 foot squared for each duck is reasonable for a night pen, so 6 would be needed fpr 2 ducks- but more space would be required if they were locked up all day as well.
If you only have a few ducks I would give them more room that the standard 3 square feet per bird. Odds are that you may want another one in the future and you won't want to rebuild then. I would give 5-6 square feet per bird so they have plenty of room to stretch, that way there is always a little extra room.
Also, if you are planning on 3 square feet per bird, you have to remember another square foot for the water, another for the nest, another for the food, etc.