If the shocks are not angled some direction, you'll lose a small amount of travel. The shock needs to form the hypotneuse of a right triangle to get the most movement through the range of motion of the rear end's up/down travel. If the truck is lowered, you're not going to get much suspension travel anyway, so the shock is just on there for decoration. Put it anywhere it's convenient- - - -it's not going to function well no matter how it's mounted.
Jerry