Warwick, if you use a swivel, the hook will always point downwards. I don't like the swivel at the back of the Nomad/Blackjack stickbaits as I fnd that the hooks just too far back for my liking, especially if I have a Jobu on. I've tended to cut them off myself.
In terms of pointing up or down, I tend to fish them pointing upwards myself but have also fished it pointing downwards and I can't say I've noticed any difference in hookup rate