That always bothered me. I can understand that they want to keep the designs simple and having hooves on everyone would look distracting, but why bother putting them on anyone at all? Just leave the "flesh knobs" on all the characters.
Because if you noticed it's easier to leave out certain types of detail. You may also notice just about every single pony has the same outline shape, the only difference is color, hair, cutie mark, eye color, etc.