A sloppy mother! I had two ducks and a chicken do that. If the poo is wet, then yes, it will wreak havoc. Poop coats and doesn't allow the babies to breathe, and it can intro bacteria.
Can they get off their nest? We made the mistake once of putting the food and water so close to the nest that our one duck just stretched and a stayed on her nest. If they're lazy or a bit over zealous, they'll do that. I increased whole corn and gave them some oatmeal. It made the poop a bit less sticky, and easier for me to fling out of the nest. Mind you, just until you get her to stop doing her business in the nest. Encourage her to get off by putting food closer, but not too close...
We had to clean off a few eggs at 14 days after one egg exploded, and another clutch at 10 days after the hen pooed on them. Warm water and soft cloth when she off. Be careful.
If she keeps doing it, don't let her brood and incu, it's just more work for you, and more potential chicks lost.
Let me know how it goes!
K Moore