My understanding is that the launchers don't run "on top" of the standard launcher, the run instead of it. So you aren't running TouchWiz and Nova, you're running Nova instead of TouchWiz. So changing your launcher could make your phone slower or faster depending on its performance and the performance of any other launcher you may use. Back in the Gingerbread days (or as I like to call it "last week" for me), there's a decent chance that a full featured, third party launcher would be slower than the stock launcher becasue it had so many more features. Now, the launchers that come with the phones have just as many of their own features that a third party launcher could be faster or slower. With the most recent, flagship phones (like the S4) there probably won't be a big difference either way.
So far I prefer Nova because it gives me an extra row of useable shortcut/widget space over what I was able to get out of TouchWiz.