I make sure that the muddy/poopy ones are not used for a 'runny' egg (so only totally heated). They are often directly used for really hardboiled polish deviled eggs since they have been cooked first thurougly, peeled, and then fried again (so heated twice) the same as Indonesian fried eggs. Wash them before use; wash my hands a lot; and don't let them being eaten by pregnant friends or children or other people that might have a weaker immunesystem.
The chances are not REALLY big that you get something from it; but every measure that can prevent it is wise. I also 'de-worm' myself weekly with a garlic-parsley-pepper soup. which strangly actually works (to my surprise as a natural-nature-medication-stuff sceptic)... Since worms/parasites are often the first thing you get from digesting poop/mud.
It may sound all a bit over the top; but if you can avoid a risk; why not? If I can chose to have a runny egg made from a clean egg or a poopy/muddy egg..why would I use the poopy/muddy egg

If there are only muddy/poopy eggs; well, no runny egg for me today and I will have to do with a double-heated one.
Unfortunately ducks are not so trainable to lay eggs on clean places haha. You can try a fake-egg, or make the entrance of the coop in a way that they can't roll the egg out, or maybe a bigger coop can work so the chances are smaller that they poop on their eggs.. or put deviders in the coop so they can't roll eggs so far... but I have given up because where they lay eggs is different from day to day.. and some JUST don't care and pop an egg out on whatever place they are at that moment, in the pool, standing on a bag of garbage, etc. and that's just ducks.