I think that other submarine versus surface ship engagements have occured, but I'm not too sure of the details. The threat was certainly there.
I posted this before, but nobody seemed to take note:
Lethal Sting
Dozens of warships and nearly 200 civilian vessels have been sunk or damaged by anti-ship missiles during the past 30 years, the largest percentage of successful ship strikes coming from aircraft.
Mostly tankers attacked by Iraqi aircraft during the Iran/Iraq war? Also, I seem to remember reading that Iranian aircraft fired missiles at tankers, and at US forces too. See
here.
Apart from the Gulf, there was at least one air attack on naval forces in Korea, during the Suez affair an RN frigate was accidentally attacked by an Israeli jet (ID problems), several US and Australian were attacked by USAF aircraft in Vietnam, some anti ship attacks during the fighting over Cyprus in the 70s, amongst other. I do not know what sort of aircraft/ship engagements took place in the Arab/Isreali or India/Pakistan conflicts.
So the threat has been proven.