You're OK. The "short barrel" Gold Dots use a different powder load that burns more completely in short barrels, but they give up nothing in longer barrels. If you're a "numbers person" like I am, you can confirm this by Googling "Ballistics by the Inch". Your Gold Dot SB ammo was compared with 10 other .40 S&W loads, and its performance is consistent with the others.
If there indeed is a .40 pistol out there with a two-inch barrel, if you compared the standard GD with the "Short Barrel" load, you would likely see more muzzle flash from the standard load, and a slightly lower velocity than the SB load.
Gold Dots in any formulation are good stuff. Go forth in peace and once you verify this ammo's function in your gun, carry it with confidence.