That is correct, it isn’t zero. But one atom per cubic meter means that even if there is an interaction between two atoms, that interaction is even more unlikely to effect a third atom another meter over.
Like, really really unlikely.
What you have here is not a compression wave. What you have is particles moving and vibrating randomly.
What you’re going to have to face here is that your intuition about how far away things are are how small quantum effects work is not likely to be correct. Your intuition will do pretty good when thinking about things your brain evolved to think about–the behavior of rocks and trees and so on.
Again, think of an experiment I could do with you.
We take a tub full of water and I drop a drop of ink into the water. A minute later I let you see the tub. Can you tell where I dropped the ink? Yes, because you can see a part of the water that is darker than the other parts, so you have a record of where I dropped the ink.
Now we take a jaccuzzi full of water. We turn on the jets. Then I take another dropper of ink and I drop some ink at some coordinates in the hot tub. We let the jets churn for an hour. Then we let you investigate the hot tub. Where did the ink drop?
There is no way for you to answer that question, even if you really could measure the location of every molecule of ink in the tub. The ink molecules are so thoroughly mixed that there is no point in the hot tub that has a higher concentration than any other. Or rather, that there places with very slightly higher concentrations than others, but these concentrations are distributed at random, and the spot where the ink dropped is no more likely to have a higher concentration than any other spot.
So even when you can measure higher concentrations down to one-molecule differences you still can’t detect the location of the ink drop.
Or to put it another way, take a deck of cards in a particular order. I cut the cards and let you examine them. You are able to reconstruct a lot of the information about the original deck. Now I shuffle them once. You still might be able to reconstruct some information about the original order.
Now I shuffle them 10 times. There is no way to reconstruct the original order of the deck after 10 shuffles just by examining the current order of the cards, because you have no way to reconstruct the many random events that happened in each of the 10 shuffles. I can let you examine the deck with any instrument you choose, and you will never be able to tell, or make any sort of guess, what the original order was.