I'm not a aeronautical engineer, so I can't answer that question. What I can say is that the explanation provided by the NTSB better fits the facts than the missile theory.
No USN ship or plane would fire a missile of any sort (dummy or not) into commercial airlanes, especially when there was the possibility of an airliner blundering into the exercise area. But even if they had gone ahead and shot the missile and accidentally hit the TWA 800, they would have come out and said that there had been a tragic accident instead of trying to cover it up. But even if they had tried to cover it up, there would be literally hundreds if not thousands of people who knew what had really happened. One of those people would have come forward and blown the lid off of the cover up by now.
The other scenario, that it was a terrorist missile, is even less likely. Shoulder-launched missiles of the type that a terrorist could acquire are heat seekers meant to shoot down hot-running jet fighters, not cool-running commercial aircraft. There's no way that a terrorist standing on Long Island could hit an aircraft 10 miles out and 13,000 feet in the air. Even if he were standing in a boat (a very small boat that was invisible to radar 10 miles out in the ocean) directly underneath the plane, the missile would almost certainly miss a target traveling at 650 mph almost two miles in the air. And even if he, by some miracle, managed to hit the plane, it would have exploded near the hottest part of the plane, the engines, and not under the center fuselage.
But why would a terrorist go to all of that trouble when he had a hundred times the chance of hitting the airplane when it was taking off? Why not just wait across the highway and shoot at the plane when it's hotter from boosting and 1,000 feet in the air instead of 13,000?
Nothing about the missile theory tracks. No part of it makes any sense whatsoever.
Much more likely IMO that it was a terrorist bomb planted under one of the seats over the main fuel tank.
Didn't anyone tell you that is against the rules? These threads are reserved for the arm chair aviation excepts and their X-Files type conspiracy theories.
I had read a copy of the NOTAM the area was cordoned due to military exercise. They picked the area to simulate interfences, radar returns, etc., from different airports in the surrounding area.