Half the time it's because if they made the graphics opaque it would block the view of the actor's faces as they interact with the interface.
Personally I think holographic and even total touchscreen interfaces dangerous because hey what happens if you lose power? You no longer have any physical controls or any way to manage the ship you're in. There need to be some physical backup controls just because of this type of situation, But in 24th century plus Trek, everything's either a holographic interface or a touchscreen.