1- Wasn't there a scan showing yata's effect fully covering itachi? I've seen fanboys using it all the time.
2-I got your point. But the thing is not seeing the shield, but what was behind him. Itachi put the shield in front of him, yet we could see him. But I got your point: we can see through spiritual things even though they're blocking the light. But that would be just an assumption, right?
3- Besides, does the shield have a mind on his own to identify what are atack and what are not? Like" oh, that's an atack, I'mma block it". "Oh, that? Nah, that's cool". If you have a shield, and you put it on your face, it will block everything that was going in that direction. If someone tells you "Hey, catch", and it hits the shield, it will be "blocked", being an atack or not.