Update!
I moved my coop and the problems with cracked and missing eggs compounded, so I did a little investigating. I'm not positive, but I think I figured out the problem! It seems that the back door that lets me collect eggs leaves a gap between the box and the back wall. I think my eggs are slipping through it and breaking! Maybe some eggs really are being eaten, but for the most part, my eggs are cracked and not eaten, so I am hopeful that a coop adjustment might fix this.