I remember reading that Nintendo designed the SNES with a hump to help prevent people from setting food and drinks on it since the NES made a great table for things to spill on. Guess they gave up when they designed the Gamecube!
First design decision was probably to improve the design, second one was when they realized that the bad design made more money when people needed to replace consoles.
I was going to say maybe it's because you can stack flat consoles and a lot of entertainment stands are easier to access the front from than the top, but you still had to access the top of the flat GCN.