Rudy and Liesel ate the apples because they couldn't bring them home without divulging where they came from. They had to hide the evidence of their crime.
That afternoon, before they returned home, Liesel and Rudy consumed six apples apiece within half an hour. At first, they entertained thoughts of sharing the fruit at their respective homes, but there was considerable danger in that. They didn’t particularly relish the opportunity of explaining just where the fruit had come from. Liesel even thought that perhaps she could get away with only telling Papa, but she didn’t want him thinking that he had a compulsive criminal on his hands. So she ate.