Behind cover does not mean 100% covered in game terms. It means you have a lesser chance of hitting them. Mechanically there are three levels of cover -- half cover, 3/4ths cover, and full cover. Only full cover means you can't be seen.
And Magic Missile can't hit Full cover either, but it's not because there's something in the way -- it's because the caster can't see the enemy so they can't target them. As long as the caster can see the target the Magic Missiles will always hit him. That is part of why it's such a useful spell.
Perfectly explained.
