To target someone with a spell you have to see them. If they're hidden, you can't see'em and and hence can't target them.
You can't just declare you're hiding anywhere. You must have cover or concealment at all times to hide. Shadows count as concealment, unless you have darkvision, which of course pretty much every non-human BBEG does, so it's often not an option (and hence the reason why it's not called "Hide in Shadows" as in previous editions).
If your player has uber stealth skillz, take a look at the rules and make him use every one of those ranks. In the Complete Adventurer, there are rules for breaking cover. They're pretty brutal. If you're darting even so much as 5 feet between cover, your check gets very hard.
And of course, there are always area effect attacks.