Wait, you are using a nipple waterer for ducks? Do you have a deep cup type water access for them at all? If not, then that is the issue... they have to be able to submerge their bills and heads to clean out their nares and eyes to stay healthy... otherwise their nares get clogged up and they can't breath... try giving her a warm bath and see if she will blow her nares out... if it looks like she is sneezing into the water, then she is working on clearing it out...
I am using a nipple waterer, but I'm aware ducks need to be able to duck their heads under, so she gets access to a water dish throughout the day on and off. It isn't constant since that just leads to a giant mess! Her nares look clean. It is worth noting I've got two other ducklings receiving the same care and they're not showing any similar symptoms.