An invisible gun, firing a torpedo is the probable way to go. I saw this idea some time ago, and thought this could work for an AI submarine.
The idea of making something invisible is something similar to what I've done getting a Kamikaze plane to fly directly into a surface ship.
The "plane" is actually a bomb, with engine sound, being carried by an invisible dive bombing plane. Least it's as invisible as I can make it. The games dive bomber won't strike the surface (unless it's shot down)......but a bomb disguised as a plane will. The two fly together as one until the dive bomber completes its dive, then releasing the Kamikaze. The path is so straight you'll never notice the release point. It appears the Kamikaze is flying in on its own....directly towards the target. I've got the hitpoints set so high on the delivery plane that it either will explode in mid air, trailing smoke to the ground (along with the visible Kamikaze plane), or it won't show damage at all (leaving no tell tail sign of it in the air).
The only draw back is when the invisible plane "drops" it's bomb. The AI gunners will continue to fire at the invisible plane as it fly's overhead. You'll see this if the Kamikaze plane is only a near miss.
If the Kamikaze is a direct hit on the sub.....game over!