I'm not gonna say "never" but I can't remember ever seeing torpedoes, dropped by AI aircraft, go under their targets, stock or otherwise. I have seen them miss a turning ship though.
And that's cuz the AI do it spot-on through the sim's AI programming. When targeting a static or straight moving ship, they drop to the correct altitude, approach angles and speed prior to the using the optimal release point from target. Human error plays a big part in most torpedo misses. Although i agree that many of the ships' boxes have unrealistically shallow drafts, i've never altered the damage boxes on any ship dp -- stock or otherwise -- to accomplish good torpedo hits. I just took a long look at how the AI did their runs and learned from that. I then used the sim's default dive bombing and ship strafing training modules to practice. Using the strafing module is pretty straightforward for this kind of thing. Your perfect approach is already set up when you load. You just have to select the right plane with torpedo besides the default Wildcat. But with the dive bombing module, i load a torpedo bomber, steer well away from the carrier target, drop low and began an approach from a good distance away to set it up correctly. I just love getting all that flak in my face as i hold an agonizingly slow 150 mph approach at 50 feet off the deck, watching that target grow in my windshield as i wait for the perfect release point!...
Rule of thumb: if you're higher that the deck of your target when you release, chances are high you'll get a
"pass under", especially if you're moving faster than 150. That's because just like in real life, if you're too high, the sim will drop the fish hard and sink it well before it begins to surface and run at striking depth. The deck of the average WWII carrier, cruiser and/or battleship is gonna be around 60-65 feet above the waterline, destroyers and transports maybe 35-45. Regardless of which you attack, you need to maintain deck level altitude and find yourself actually having to pop up OVER the target after release. This will prevent the fish from dropping hard and sinking/running below the draft.
But like Shadow Wolf said, missing evading ships is another thing altogether. The AI don't compensate for that very well, but a human can.