It does - if you don't use abilities you won't get the 2m Stoic bonus at the end, so in theory an SS score will always be higher than an S.
I've noticed there's a Critial Charter Bonus of 50 Rhythmia as well the first time you max out your critical progress on a song. It's a one-off for each song, but your critical meter for that song then gets a permanent gold crown on it. So that's another thing to aim for.
If there really is an SSS rank then I'm going to have to go for that. I was wondering if there was a medal or something, similar to Perfect Chain for hitting every note.
If that's true, then I guess you haven't properly "beaten" the game until you've managed to SSS every song on Ultimate... which I think would require the reflexes of a demon.
Now with 80% more Cthulhu!