Hi, welcome to BYC!
I just hate dirty eggs or poopy chickens. And dirty lay boxes are nasty.
But aside from that, rats are chicken predators. I prefer mine OFF the ground.
Only reason for a chicken to sleep in the nesting box at my place is to hatch eggs or raise chicks. But broody's DON'T poo in the box.
The chicken vent turns inside out so that eggs never touch feces when being laid by the chicken, except what they come in contact with once laid. Avoiding e-coli and other contaminants is reason enough for me. The eggs have a protective layer that helps them stay fresher longer if you don't wash it off. But if it's compromised by being soiled when laid then it defeats the purpose. So your eggs will lose their freshness faster. And who wants to eat eggs that had poo on them, washed or not?
Anyways, that's just me. Like Azygous said... most things in animal rearing are about personal choice. I will also note that soiled eggs have a lower hatch rate, showing it does indeed have SOME impact on the eggs.