It solely depends, it's about performance and image quality. More pixel pipelines mean good quality and resolution and clock speed is for performance.
It has more to do with the clock speed being higher. Given the fact that the limiting factor in todays GPU's is memory bandwidth and Shader Unit performance.. it's no surprise to see the 6800GS beat a 6800GT with mearly a clock increase on the GPU. This clock increases is also clocking up the shader units. Therefore they can work quicker at processing Pixel shader information. Eventhough the Fillrate is lower on the 6800GS while the memory bandwidth is the same, the extra clockspeed speeds up things internally.
Given the fact it was also built on a 0.11u process (vs the 0.13u process for the 6800GT GPU's) it is able to overclock significantly higher then it's 6800GT brother while remaining relatively cool (less voltage is needed to power a smaller die then a larger die... voltage = heat. Heat hinders the performance of electronics).