Drilling the waterbox is to increase airflow. It's done to allow the air to flow better in the stock 650 waterbox while running the larger 750 motor. This has nothing to do with weight.
The only thing you can do about the weight is to throw away the heavy stock rubber mounts, replacing them with something lighter, and buying an aluminum waterbox. The stocker is stainless so it is much heavier.
Drilling is not done for saving weight, and will not save anything worth wild.