I don't go through the head or upper part of the body. I like to thread them on the jig but just at the last legs then thread them on like usual. I don't care if they are dead, I've used black dead worms and caught fish just fine. It's the leaky scent and jig action that gets the bite. On spoons with treble hooks, I will pierce the body just behind or at the last legs, then pierce another barb through the back of the body so the worm is laying horizontally. Sometimes I will hang another worm pierced through the head on the 3rd barb. With vertical drop jig with a single hook, I'll pierce the body at the last legs then push it all the way around to the jig body, then pierce the body again so the worm hangs horizontally again.
I like the worm hanging horizontally for a few reasons. My flasher picks it up better on thin drop jigs, with multiple stabs it leaks a lot of scent, it hides the hook better and I think it tends to get stripped less often.