One theory for no claims is that terrorists hit the wrong plane. An El-Al 747 was supposed to be in front of TWA 800 but had a ground delay. Would a terrorist organization admit to shooting down the wrong airplane?
Of course they'd take credit. However, in that case, they'd just claim that they were intending to target the American plane all along. Back then, shooting down an American 747 would have been just as good as shooting down an Israeli 747, for pushing a terrorist ideology. Today, of course, it would be even better.
No self-respecting terror organization would go to all that effort, technical and otherwise, and then allow the Americans to explain it away and pretend it didn't happen. What's the point of a terrorist act, if nobody knows about it? Hell, they even claim stuff they didn't do.
Not saying that the NTSB got it right, but that's the problem with conspiracy theories--you start with your conclusion, and then bend every fact to try to make it fit. (Of course, that problem exists with all flawed investigations or flawed scientific theory.)
Bubba