It's hard to tell. If it does, it's not doing much... the difference I've noticed between near 100% plays with the same distribution of hits and one player using a mod, is typically around 200 points. Which could just as well have happened in normal play.
In any case, the description of scoring on the wiki makes it clear that mods won't do anything for SS plays. Which means that mods are apparently for people that are less capable of playing a song perfectly. Thinking about it now, it occurs to me that this could have been fixed by increasing the value of 300s when mods are applied (moving them up a bit towards the 320 of MAXs). But it's probably too late for a change like that now.