Memory frequency has very little to do with performance. Latency (or timings if you prefer) has a bit larger impact, so that 1333 @CL8 is probably going to be faster than 1600@CL9.
As to the performance hit when running 4GB on a triple-channel controller, I really have no real idea. I would not expect anything huge, but I would expect something measurable... I would expect tri-channel 1333 CL8 to give you more FPS in a game than two sticks of 1600 CL7 in the same board. Not a lot of FPS difference but a few frames anyway.