(1) is referring to a present situation. This person you are talking about or pointing to cannot be Mary because I know that Mary is far away. In the future Mary may come back from New York so that someone you see on the street COULD be Mary, but that has nothing to do with the person that you are pointing to right now.
The use of the word "never" in (3) indicates that the person is not now, and for all time cannot be, a good shepherd. Of course the speaker might be wrong: maybe you can train or study or whatever and become a good shepherd. But the speaker believes that you never will.
(2) may be ambiguous. I think the most obvious reading is that the person is not now and never will be a good shepherd. "Can't" means that it is not within the person's ability. But as stated it doesn't rule out a change in the future. It would be quite reasonable to say, "You can't be a good shepherd as long as you show so little concern for the sheep, but if you changed your attitude, you could become a good shepherd."
Saying someone "can not" do something is much stronger than saying he "is not" doing it. If the speaker said, "You are not a good shepherd", that would leave the possibility of the person becoming a good shepherd in the future much more open.