According to some real examples, it looks like even with usb, there is no discernible input lag.
This is by no means conclusive, but I believe most consoles poll input from controllers on each frame. which is ever 17 ish ms(for 60hz). There is some lag inherent in usb but not enough to miss a poll on frame, but if it does you'd never be more than a frame off from the time you pushed the button, even with original console it is possible to miss an input poll, causing your input to be polled on the next frame. Actual oscilloscope tests have been conducted which can measure the tiny amount of lag in usb. While the best approach is always zero latency in retro consoles, here we see what I would argue is a reasonable amount of lag. An amount that can only be measured with expensive equipment and not humanly discerned. Of course, best is original. This is my rudimentary understanding of input latency, what is best I think would be for you would be to try it out for yourself. The upcoming add ons will ensure 100% that input will be best possible. But if you can run the original system next to MISTer with it's existing usb setup and the result is identical...