Snakes are head shy because it is their instinct to protect it. It's what keeps them alive, just like you and I will protect our heads when falling, or something is falling on us. Boxers protect their face, snake ball up with their head in the middle to protect it from certain damage.

As they learn to not fear us, they wont be as head shy. Some will overcome it, some wont. Depends on the snake.
I can see where the vet makes that conclusion, because the snake is trying to protect it's head from a scratching biting rat, but most often, the snake strikes the head, so nothing to worry about other than some foot scratches. Some may react to this by being head shy, but I certainly dont think it is a normal thing (to develop head shyness).

Just a BP behaving like a BP. Or snake for that matter.