I'd just tried turning off layers off in Zelda 3 and you're right nes, it doesn't magically turn light on. So I was wrong on that game but it works well with SMW2 Yoshi's Island as you can see on those 2 screenshots
Screenshot 1 : All layers turned on
Screenshot 2 : Layer 3 off
It's not really usefull here but it's the first level where I was able to produce the effect
For Zelda 3 , I think I used to play with the layers to make visible the invisible floors in some castles (those floors were visible only when you were lighting on all the torch in a room or for a small amount of time when you were using the magic "ether")
This is also a usefull option to capture and edit sprites.