In UMK3 there is a 3 second recharge time for his missiles, if you do a single, you can't do a single or a double for 3 seconds, if you do a double, you also cannot do a single or a double for 3 seconds. In MK3, you can continuously do singles, and the double has a 3 second recharge, however, it doesn't effect the single. You are also forgetting that the missiles move Jax backwards as well. It would be stupid for Jax to throw missiles in a specific pattern but he can throw a single any time he wants which makes up for the zoning.