I had a feeling the polling rate was probably to do with the frame rate of the SNES rather than some requirement of the controller. I'll try out a higher polling rate and see what happens.
Yeah I wouldn't be worried about the hardware at all. The only chips on there are two 8-bit shift registers and according to the datasheet at 5V they can run up to 3MHz. You're much more likely to run into the limits of the USB protocol than the SNES controller hardware.
