Instead of thinking of it as the chakra system, think of it as the nerves system. I could punch you in your chest and not cause you heart to skip. Someone said above why not just send a lot of chakra at the heart and do damage that way, well if a person is hit hard enough his hart could stop and the person would die. Now imagine that I could create an electrical charge that about four inches long from my hands. Then, I would be able to send an electrical charge strait to your heart. As far as the chakra holes think of being hit in the arm it hurts a little but if I send an electrical charge to your nerve ending you will most likely loose the use of that whole nerve and whatever part of your body that nerve controls.