This sentence is a little confusing but I gather it to mean that you're forced to shoot at nothing. You should not be penalized for this, the only thing really penalized here is not taking the fastest known route. From what I could tell, the speed is constant in Space Megaforce, like most vert shooters. The only thing that can be done more quickly in a Space Megaforce run would be the speed at which menu/input options are chosen, and how quickly you kill a boss.
I also started a run for this game but I haven't touched it in a while; seems we both determined the rotating green balls would be the most efficient weapon (since you can freeze them in place). Best of luck; hope to see a WIP soon.