You're right, that is a bit odd and should probably be fixed (if you're sure it didn't count... I can't see how it possibly couldn't because the arrow hit and there's no reason to have a body hitbox extending that far).
The OP doesn't talk about though. This topic is about extending the headshot hitbox to the neck, which would be stupid, because there is no brain in the horse neck and the respiratory and circulatory systems are based in the chest, not the neck.
I don't think it's so hard to hit a horse head; it's about the size of a human chest and movement speed should not be a serious obstacle to your accuracy. Worry about acceleration/manouevrability, which believe it or not, infantry has in spades.