Absolutely everything you change on a guitar makes a difference. How big it is and whether you can detect is is another matter. You also have to consider whether the difference is better or worse.
There is a huge difference between electric and acoustic instruments on this as well. I wouldn't worry much about what finish on an electric. I do consider carefully what I use on an acoustic instrument. It has to do with the way the sound is generated. With an electric most is the string and the pickup, with the body materials and fittings adding some degree of timbre. On an acoustic instrument the body alone is moving the air so the material properties become far more critical.