Then why use it or even develop it? Especially in the mid-1990's when submarines can dive deeper, run quieter, move faster, and maneuver easier than the subs of World War II? Such a weapon makes zero sense, and any submariner would confirm.
The information I read said that the Navy immediately abandoned 'testing' of the 'missile technology' they were using at the time.
So far the only documentation I can find was a mention of trying to fit their ground-based AA missile to a sub. Those things were too large, and couldn't really take exposure to water at all, let alone at depth.
I would have really hated to be a German submariner after the first half of WWII.
"On display, according to Graduates source, was a secret anti-aircraft missile developed for the Seawolf class of attack submarines. The Navy planned to use the missile to defend the subs when sailing ahead of the fleet without air cover, especially in shallow water when vulnerable to shore-based defenses."
Read more at http://www.wnd.com/2013/01/is-u-s-navy-coming-clean-on-twa-800/#W3sVHu9k5wLTs9fD.99
I'm still hunting the AA missiles. Maybe those were manufactured in my mind based upon these. That aside, it isn't much of stretch to assume anti-aircraft missiles could be fired from a sub, given the fact that cruse missiles can be fired from torpedo tubes. Germany was developing self-guided AA missiles. Given today's electronics, it isn't difficult to image a guidance system locating aircraft autonomously.
Still, there is no reason whatsoever to suspect such a thing in the TWA800 incident.