Why doesn't Patchwerk take fatigue damage?
This is intentional. The bosses in Adventure Mode don't always play by the rules.
Patchwerk starts with no deck but he does not attempt to draw a card at the start of his turn. This means he won't normally take fatigue damage.
However, Patchwerk is not immune to fatigue. If an effect does cause him to draw cards, such as Coldlight Oracle's battlecry, he will attempt to draw them and take fatigue damage as a normal player would.