Based on some of the information from the new documentary, it is possible that there is a cover up of real information about the 1996 TWA Flight 800 crash. Unfortunately there is no way to know for sure, because the supposition is based on investigator opinions that they did not find any reason for the crash, which makes it difficult to determine if they overlooked or lacked the technology at the time to determine the cause or if there was a real cover up.
I generally don't believe conspiracy theories because they often lack evidence. Much of the plane was recovered, but no missile debris. No one saw a missile being launched. (they saw a streak only, which could have been many things) When it comes down to it, most conspiracies theories can be debunked.