Not many natural places have clear water. Usually there is all sorts of material suspended in the water, blurring, obscuring sight. Swimming pools are constantly filtered, or you wouldn't see much in them at all...
The air-water boundry bends light as it passes through it. Is this equivalent to an illusionary effect, or does the missile follow the path of the light?
Personally, I'd prefer magic missiles not penetrate the surface of the water. But that's just me. I really, really detest how the DnD 3.x RAW have dealt with underwater scenarios.