After reading the September issue of Motor magazine I'm pretty sure I have your answer!

Apparently the Le Mans racing Porsche 917's of the 1960's had holes drilled in the key to cut down the cars total body weight, so it stands to reason that since pinballs are also heavy that this is also the reason for the holes in your apron.........you're welcome!   

LOL Well that's a winner! I am going to drill all my machine keys to make them lighter, will make it much easier for moving them around! :)