with bait you will hook more fish deeper because they are trying to swallow the bait. with flies, any bite from a fish is instantly transmitted to the rod so there is less chance of hooking deep. I can't honestly say with spoons and spinners cause I dont fish with them much, but I think more damage would be done by the treble hooks than any thing else.

I have heard that fishing with yarn attached to the hooks helps in hooking fish because it gets stuck on their teeth and on their tounge which also sounds to me like it would also help keep them from swallowing it.