I'm pretty sure it wasn't because of no 3D-effect that Cubic Ninja didn't do well.
I find it funny that many of those who don't like the 3D-effect are now complaining that companies may not actually use it in some of their games. They hate because they want a reason to hate. It's like complaining that a 2D (not 3D with no 3D-effect) game was on a 3D-capable system when the emphasis of the system was that it can render a bunch of polygons to make 3D environments. Yet, some of the best and most beautiful games on those systems are 2D. Not every game can use the 3D-effect effectively. If a game is not designed to work well with the 3D-effect, then it should not be forced to use it, just like with the touch-screen, WiFi, etc. As others have said, if a game doesn't use it, then that frees up system resources as it is not rendering 2 frames every screen refresh.
If developers wanted to (and if the system is designed for it), they could still have the system render 2 frames every refresh, but not activate the parallax barrier, so that instead of displaying a 400x240 image, it'll act like an 800x240 image.