This is one of those conspiracies that always seemed probably true, based on my cursory examination of the evidence. Or the other way, assume a weapons test went horribly wrong; what would the result be?
Missile damage to aircraft leaves very distinct and VERY obvious traces as you would expect from a bunch of shrapnel suddenly slicing through the fuselage at hundreds of different points. If you want an example look at the reconstructed fuselage Malaysia Airlines Flight 17 which got shot down over Ukraine. 95% of the fuselage of TWA 800 was recovered. It was not hit by a surface to air a missile.
(“The IAMAW strongly criticized the FBI's conduct during the investigation, including the undocumented removal by FBI agents of wreckage from the hangar where it was stored”, from the Wikipedia link above.)