TWA 800 broke apart as a result of a major overpressure event. The particular mode of in-flight failure observed in TWA 800 is very difficult to cause by poking a single missile sized hole anywhere in the aircraft. Not theoretically impossible, but difficult to the point that it's not a reasonable explanation. You have to take the combined probability of 2 very unlikely events rather than just 1.
Seems you know of data about commercial airline fuel tank spark explosions. I didn't find much about this problem online. When else did this seemingly under-reported catastrophic commercial airline event happen?
https://en.wikipedia.org/wiki/Thai_Airways_International_Fli...
https://en.wikipedia.org/wiki/Pan_Am_Flight_214
All fuel tank explosions. Modern aircraft have equipment specifically to mitigate fuel vapor in the tanks because of these sorts of incidents.
TWA 800 also caused improved maintenance requirements of wiring that might arc/spark, as inspections of other aircraft found widespread metal shavings, non-standard wiring, and eroded insulation in nearly every aircraft they took a look at.
Why not? Inert missile punches through a fuel tank, aerosolizing the fuel, and either the missile engine or a damaged aircraft engine ignites it.