One of the first 3D launch titles, Super Stardust HD is a 1080p game, but was downscaled to 720p so that performance wasn't affected. Sony’s senior development manager, Simon Benson said that if 3D games did run at 1080p framerates would drop, so instead it will split any native 1080p titles into two 720p images so that they can still run games at 60fps.
Sony says that the difference won't even be noticeable.
3D Blu-Ray movies will still run at 1080p, but obviosuly video games are far more hardware intensive. Are you bothered about not getting the full HD experience?