A long time ago I installed a sound-hole pup to an acoustic and put a volume pot and a tone pot on the sound board. I didn't notice any difference in tone at all. A few years ago I removed the pup and pots leaving the two holes in the soundboard. I didn't notice any difference in tone at all.
Was there actually a difference? Enough to be measured by some sensitive equipment? Maybe. I don't know. And I don't care because I couldn't hear any difference, and that's what matters.