It says
Look at the top tree cards... Draw one...
Having 2 cards left, you would look at the 2 of them and pick which one to draw and discard the other, no fatigue taken.
Having 1 card left, you would look at that card and draw it, being the lone card left, there's no option for you to choose from. No fatigue taken either (as Studoku confirms in his answer).
Having no card left, you don't take a fatigue hit, since you can't look up at any cards, you can't draw one, no fatigue.
As you can see from the screenshot of my testing, my health haven't changed after playing the second one with no more cards.
Looking at cards doesn't count as drawing them, neither is discarding them considered a draw attempt.
Note that fatigue is represented as a card but it's not a card at all, it's just the way Blizzard decided to represent it. It could have been a stabbing dagger, a chicken biting you or whatever... so don't mistake the look fatigue got with it being anything but a effect of having no more card and having to draw one.
Best Answer
No, Chromaggus does not cause you to take any extra fatigue damage. The wording of the card is "Whenever you draw a card, put another copy into your hand." It doesn't add extra card draws, it only duplicates the card after it is drawn.
In the official BRM reveal stream, they go into fatigue with Chromaggus on the board and only take a single fatigue hit.
Skip to minute 54 to see the play in question. http://www.twitch.tv/playhearthstone/c/6438751