It makes sense that a lacquer finish will probably settle in into the wood and even wear down thinner with use, allowing the wood to resonate more freely and thus sound better.

As for what happens to the wood itself, I can only surmise that vibrations over time will cause all the components (neck, top, body) to ’sit in’ more snugly against each other, and it’s this improved contact that allows better translation of vibrations. Possibly even slight changes in moisture content of the wood will cause slight changes in tone, but drastic moisture changes are always bad for your guitar.

At the end, improvements in tone will be due more to the increasing skill of a guitar player over time, than any physical changes in the wood or finish.