HOLES in crackers are there for a reason, not just for decoration. Without these holes the biscuits wouldn’t bake correctly. They allow steam to escape during cooking. This keeps the crackers flat, instead of rising like a normal biscuit as the steam tries to escape. They also help to properly crisp the crackers.
The holes’ positioning and number varies depending on the size and shape of the cracker. If the holes are too close together, the cracker will end up being extra dry and hard, due to too much steam escaping. If they are too far apart bubbles will form as parts of the cracker rise.