I've checked various "updated" season 2 episodes and have yet to see the comet tail logo. From what I recall, though, not all pre-movie international episodes have the Nickelodeon logo, it's mostly season 3 and beyond from what I remember. But I might be totally wrong.
Unfortunately, I only have seasons 1 and 2 purchased on my current active iTunes account. So I can't check whether the season 3 episodes have it or not. It would really help if the episode "Something Smells" was updated, as the defining feature distinguishing the American version from international English prints is the "Hi Building" audio glitch*.
It doesn't mean the episode won't ever be updated though. Ever since my earlier post they've already updated "Prehibernation Week / Life of Crime", "Grandma's Kisses / Squidville", "No Free Rides / I'm Your Biggest Fanatic", "Pressure / The Smoking Peanut", "Shanghaied / Gary Takes a Bath", and "Sailor Mouth / Artist Unknown". So it looks like they aren't stopping this refresh any time soon.
*Here's a little tangent: Being Canadian myself, and only having seen either the international print or DVD version of Something Smells for much of my childhood, I never even knew there was a "proper" version of the episode until one time I discovered the American version uploaded to Youtube by some user who recorded it off Nick USA. Then, after purchasing season 2 off iTunes for the first time I felt so happy to finally have this version. It was like watching a pre-movie episode I've never seen before.