I think it's less about them discontinuing a part and more about that part being superseded by an updated version. This happens with all manufacturers of bikes, cars, airplanes, what have you. It's just usually you're dealing with a mechanical part that has little to do with how the bike looks. Keep in mind, these have to be a direct fitment, so something like the GTs headlights would not supersede the ST projectors.
That all said, it sounds like they did right by you.
I'm confused about the difference in the fairings, though - on any photo from any year ST I can find (and also on my GT), all of the vents under the swoosh on both sides are very clearly triangular, not square shaped... Can you post a photo of what you got?
EDIT: Nevermind, I see what you mean, now. You're talking about the vent behind the swoosh, not the vents under it (on the bottom of the fairing). I hadn't noticed that before.
Last edited by XL1200R; 11-21-2012 at 10:27 AM.