The majority of the stopping power comes from the front brakes. With the more powerful (and usually larger and more heavy) AMG models, you do need more powerful brakes than the smaller, lighter, less powerful models. The higher number of pistons used in the front brakes of the higher end models probably equates to more clamping pressure on the rotors (although I'm not entirely sure about that, as BMW continues to use a very simple braking setup and gets equally good, if not superior stopping distances for their M cars).

Having said all that, I'm sure another reason is "marketing". There is a huge price difference between the C55 AMG (4 piston in the front and 2 piston in the rear) and the ultimate SL65 or S65 AMG, and I'm sure they want to make sure the potential buyer of an SL65 or S65 feel like he is getting the absolute best brakes possible. Another factor is cosmetics. Larger, more fancy brakes LOOK better visually and is another part of the "bling" factor.