I use them to mark the eggs under my broody hens. I draw multiple circles around the width of the egg, so it can easily be seen no matter the angle. I don't have 3 legged, 2 headed or tarded chicks hatch, so I'm thinking it's alright.
I used sharpie on a couple eggs that I have in my bator before thinking better of it, eggs are porous and who knows what chemicals might leech through. Surprisingly they seem to be progressing well!! We'll see how they hatch.