i'm a little surprised you saw a difference with the 3GS.. could have been something else. the theory back then was the 3GS was built to be jailbroken mainly because of the RAM
i know when i had my 3G and whenever installed winterboard it made an already slow device even WORSE. when i jailbroke my iP4 i purposely waited a while before installing winterboard to see if it would hinder performance and the answer was No. unless you're runnning animated wallpapers and whatnot, i don't see there being an issue with the iP4
tbh, there are a too many other apps/tweaks out there that need to be worried about than winterboard. in my experience anyways