Submarines don't have surface to air missiles, for obvious reasons. Shooting it off gives away their position. And how would a submerged submarine know there was an airplane around to shoot at and how would they aim the missile?
Submarines can surface and they definitely can launch nuclear weapons. But you could be right - I'm certainly no expert.
But I assume there are Navy ships that are capable of launching a SAM and, as I recall, there was a Naval exercise being conducted in the area at the time of the shoot-down.
Was it ever determined if naval maneuvers were operating in the area? Were there no witnesses out there on the ocean? No interviews? Did any ship involved in that have surface to air capabilities? Did they look at the inventories to see if any missiles were missing?
They must have asked these questions.
Actually there are several systems for subs to launch surface to air missiles. And it is certainly possible that one was being tested.... however terrorism is more likely.