I updated to 3.3a when it was originally released before i even knew about the homebrew scene here, a week before the fixed twilight hack was released.... then i learned of it, installed the new twilight and i've left it as is from then until currently... i then purchased a new original copy of brawl, and it asked for nothing, no updates.... didn't even ask me for an arm, or a leg, or my first born child.
it's harmless update. if nothing else your twilight hack would have to be updated to the 3.3, but it's already been stated that brawl carries the 3.2 update, so, it simply needs the files contained to run..