If I paint on hard boiled eggs with actual paint (acrylic) will it harm the actual egg inside?

There shouldn't be much of a problem. The reason some eggs turn color is because the shell is semi-permeable, which means it lefts some air and water through to help the chick inside grow (even if there isn't a chick inside). Acrylic paints are usually a) non-toxic, and b) very fast drying, so you shouldn't get sick if you eat an egg painted with acrylics.