Just to point out a few issues with your argument:
1) It's a game.; Not real life. This has been noted about 18,000 times. Because it's a game, the sub has some characteristics similar to all the other ships in the game. It's referred to as playability.
2) Your salvo (or you assume all shells actually hit the sub) DID cause significant damage. As the BB player, you don't see how much damage was caused, but I can assure you that it is not trivial. A sub that is burning and has to crash dive will be "game over" real quick, so the sub's defenses are in jeopardy and most subs do not carry a repairman, so their repair rate is trivial. If the burn rate drops their durability below a certain threshold, then have to surface...Boom ...game over.
3) Not all BBs have powerful guns. Unless you're hurtling 2500 HE shells, a lot of them are absorbed by armor. Maybe you loaded AP on your shot. That's not gonna hurt as much either.
4) Accuracy? Rarely does a salvo hit full broadside all shells. A sub is small and most shells land nearby, doing nothing. Don't claim that all your shells landed solidly, most don't.
Let's switch topics and have you defend why it takes 12-18 solid mid-ship torpedoes to bring down a BB5 from a sub when those torps contain around 20K HE each.
Also, please explain why a sub should even run out of air in less than 4 minutes, when real subs could remain underwater indefinitely with snorkels.
But to answer your questions more directly, the reason the upper tier subs can take more damage and still motor is the same reason a Lion II can take more damage than a BB1 or CA. A CV1 can be sunk with a Neutral Frigate, a Heavy Cruiser or BB1 will have a problem with a PCV or CV6, loaded up with PHH or guns. Ever see a CL take a full salvo from a QV and survive? Of course not. Have you ever seen a BB5 or BB6 take a full salvo and not sink? Shouldn't that be subject to the same unrealistic expectations? Should BBs be capable of taking 10+ torps and still OH at 42 knots as if nothing happened, all guns blazing away?
It's a game. Toy ships in a small lake. It's all ridiculous and you just have to assume it's flaws.
