I think if you do succeed at getting the headshot and the enemy is unarmoured or in a spot that hits the skin you deserve a reward for the accuracy which should be instant death.
This, to a degree. Though it would be difficult to build a "hit box" around the armor, it is absolutely possible. If your arms are exposed... Well, they're exposed and they're a fine target. Crippling should be instigated through damage to the joints, not the limbs themselves. Oh man, I'm sorry guys... But an arrow in the knee is a lot more damaging than an arrow to the thigh.
Armor would be the biggest variable to a successful headshot/crippling shot. Fur and leather could possibly have a 50/50 chance of penetration. Steel, iron or the other "hard" armors could use a 80/20 chance of successful penetration. 80% of the time, the arrow may hit at such an angle that a metallic helmet could easily deflect it.
The biggest difficulty would be balancing that with the armors themselves. Locational crippling by a successful hit is a must, but the armors should respectively follow the same 50/50 paradigm for soft armors and the 80/20 paradigm for hardened armors.
EDIT: Unfortunately, clothes or robes would offer no protection against penetration and would be entirely for the roleplay value.
EDIT2: Perhaps a thigh/leg shot could slow you down for 5 seconds, or a shoulder/arm shot could slow down bow draw speed and weapon swing speed.
EDIT3: A successful joint shot would end in a crippling blow outright.
Haha, EDIT4: How about if you get clubbed in the head it could blur your vision for 5 seconds too? That'd cause a realistic amount of disorrientation.