Assuming there is a difference (and believe me, there is), would you really notice? After all, you are in the midst of a game, and the last thing you mind does is go "I say, that fellow over yonder seems to be a tad hard to mark with this here fine piece of paintball apparatus. Oh, I see now, he is a wee on the smallish side of things..."
Instead your brain just goes "Waaaaaaaaaaah! Murder! Death! Kill!"
The only moment you would really notice a player is small, is when they run form bunker to bunker, and only if you have other people within view as reference. The reason you don't notice it's harder to hit the smaller guys (assuming they have the skills to go with it) is because you hardly see them, because they are naturally more able to play tight.
Being over 6 feet, and somewhat on the heavy side of things, I'd like to think it doesn't make a difference, but it does. What do you think the Luftwaffe had more trouble with, a small, zippy P51 fighter, or a large, ponderous B17 bomber?