Since I can't control the quality of the eggs going in, only of the process, I have no qualms about charging per egg. Since I will have my own eggs in the 'bator as well, it's always my goal to ensure optimal hatching conditions. If someone were to bring 100 shipped eggs that all failed to hatch, or eggs from an infertile flock, that should not negatively impact the value of the service I perform on the eggs.
That's not an issue for me as I don't sell chicks (though I do sell poults). I only sell surplus poults, so again it won't impact my market. And if I hatch quail, guineas, bantams, pheasant, ducks that I don't raise then it definitely has zero impact.