I think this is one of those things that would be hard, if not impossible, to get numbers on. It's likely that more players overall stick to vanilla configuration options, but it many games, long-term players are more likely to mod. I think I recall back when GameSparks was added, it was stated that data wasn't collected from modded games but I'm not sure.
I think many, if not most, of us who regularly use mods just don't say much about the stuff we're changing. I currently use a backpack mod and several other things, but I never complain about the stuff in vanilla not being what I want because... I can just change it. LOL I would struggle to play without a backpack mod at this point, but I don't think TFP should change it, because it's still a survival game even if I don't always play it like one.
I would like to see more things like backpack size (both bigger and smaller) eventually added to the vanilla in-game configuration options just to make different ways of playing more accessible (I was over the moon when the Bloodmoon frequency options were added), but not right now because I think it would muddy the waters too much before other features are in / complete.