Shadow ponies have an ability to hide from their foes extremely efficient. They can use the shadows around them to just hide "behind" these, and remain unnoticed while being touched by light. However, they can't alter their environment by doing so, as they live only in the darkness (and not Darkness).
That is the difference between Shadow and Darkness. They are both filled with dark, and that's why Shadow is considered "darkness". But Darkness goes on with Badness, and it's the total opposite of Good and light. Shadow could and should be considered as what is hidden from Light, and Darkness as what is opposite of Light.