I did a science project on hatching eggs. We marked half with pencil and half with sharpie. It really doesn't make a difference unless the sharpie covers more than half the egg. If its just a question mark, it shouldn't hurt any.
For what it's worth. I used a sharpie on some eggs under a broody and all 5 hatched out just fine. If I were going to use the bator I would probably use a pencil though.