Or if you're talking about the "completing the game with only ??? babies" achievement, you just have to pick the third unknown baby option after completing a level everytime, all the way until you beat chapter 3
yeah hidden babies are just the 3rd (4th if you have more options) baby pick, the one that's "hidden" with ???, so for the unlock you just have to beat a run while always picking the unknown baby option, i'm not sure if getting crystal ball prevents you from getting the unlock or not