Your body just craps out the excess. I am sure Trouble could add some more info on this one. But as far as it working against your muscle building it doesnt. The more the better and what your body cant use its going to go else where.
It depends on how much protein you are concurrently taking apart from the shakes, and on your height, weight, sex, and goals. And yes the body is fully capable of storing excess protein as fat especially if its receiving an adequete amount of Carbs and Fat.
I drink 2 a day, sometimes 3. 1 scoop of whey is usually around 120-130 calories. Big deal. I really don't think anyone is going to get fat off an extra shake.
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