The way the NES and SNES work is that once per frame you read from the memory address mapped to the shift register to get all the bits out, one at a time. For certain inputs you only care if it's pressed now. Others you compare to previous state to see if it changed.
Bounce could, theoretically, cause an input to be read as a non-input if it just bounced at exactly the wrong time, but it won't cause multiple inputs, as it's only polled every 1/60th of a second.
Yes, it sounds like SNES implements debounce by just scanning slowly, but if you want to feed USB reports at maximum (or above maximum) specification, you will want to check the state more frequently, and you'll need an alternate mitigation for switch bounce.
Bounce could, theoretically, cause an input to be read as a non-input if it just bounced at exactly the wrong time, but it won't cause multiple inputs, as it's only polled every 1/60th of a second.