I did sub challenge 1 & 2, didn't try 3. It's easy enough once you learn some tricks. Fire off a spread against the clusters (especially on challenge 2) to do a little initial damage or cause ships to scatter and make it harder for the destroyers to steer around, but for your specific targets, get in front or behind them and hit them in the screws or the front hull. Even if they turn you'll still hit the hull somewhere and cause damage. Then haul ass far away and resurface to get more air. Go back down to depth 3, sink to 4 to confuse the destroyers, then come back up to 2 and repeat the process.
It's just a matter of confusing the destroyers, I've found it's easier to get them to chase you and just release your rear torpedos right into them. As before, they will still get hit even if they turn, just make sure you are close enough (like within 0.2-0.3).
I really love the sub missions. Sucks there's so few of them. They should just put out an entire sub campaign game. Maybe a historical one with old WWII subs all the way up to modern nuclear subs.