I can't say exactly how it applies to BG2, but in d&d when you enter the shadows you have to roll to "move silently". If you fail your "move silently" roll, you may still be in the shadows but others will be alert to your presence.
I guess in a way it's similar to the effect of a character that has the "improved invisibilty" spell on him that is attacking. Enemies know that he's there, but can't lock any spells onto him and receive a severe penalty when attacking.
Move silently just goes hand in hand with hiding in shadows. You can't have one without the other. You can be hiding all you want, but when you move you're going to make noise...
However, that's just coming from d&d experience... i don't know how exactly this is transferred to BG2.
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