The two balls combined, moving at say 1200 fps, would have the same energy as a conical that weighed 2x the weight of a single ball, assuming the conical was also moving at 1200 fps.

So the target would be struck with the same engery, yes. That energy would be spread out over 2x as much area with the balls, as compared to the conical, and so the conical would out-penetrate the balls.