Yes, keeping their coop clean is hard enough, so I picked something that they couldn't splash around in.
My first set of ducks (runners and campbells) had no problem with it. My second set (pekins) started getting dirty eyes, but I only had them in the coop for two weeks (I bought them older and allowed them to free range at a younger age). My third set (runners) have no problem with it. So in my experience it depends on the breed. The pekins developed problems quickly, the runners never did. In fact, my first set of runners/campbells stayed in that coop for about 8 months. 8 months drinking from a nipple with no eye problems, compared to about a week before problems for the pekins started showing up.
Once my ducks are big enough to free range they have three options for water: a nipple feeder, a bin of water that I refill daily, and the pond that I am currently digging.
You are going to have lots of problems if you continue on raising ducks without a bathable water source for eight months. Just a warning.