ive tried it without any more success than hooking through the mouth. i would think you would miss more fish - from what i understand (and im no biologist) walleyes strike towards the head of their prey (head first). but who knows - when i bobber fish with little kids in the boat they can bait a minnow through the stomach and catch more fish than me.
Not sure about this, but I remember reading an article on how the 'eyes eat. From what I remember, they eat tail first but when the bait is in their mouths, they flip it around and swallow it head first. It is during the flip that a lot of people will try to set the hook and that is when they lose the fish. I am not sure if hooking by the tail works better or not on a jig. I have often hooked minnows in the tail on a plain or colored hook with mixed results. Seems that whether hooking through the tail or head or back does not seem to make a difference if they are eating. BUT, if it is a tough bite, you are going to want to make the bait appear as natural as possible and hooking through the lips and slowly retrieving is the way to go.