Yeah I too wondered why the author would target 60Hz at all. The fact that the SNES controller is polled at 60Hz is simply a consequence of the game reading the input at that rate. As mentioned in the other comment in this setup the polling of the controller is not in sync with the game reading the input at all. Thus even if you target a polling rate of 60Hz perfectly you'd actually have worse input latency than the original hardware.
It would be much better to target 120Hz or higher to reduce input latency and bring it as close to the original hardware as possible by ensuring there is always an up-to-date input state ready for the game to read.
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.
It would be much better to target 120Hz or higher to reduce input latency and bring it as close to the original hardware as possible by ensuring there is always an up-to-date input state ready for the game to read.