Yes, groundfiring subs is unintuitive, created by engine limitations, unhealthy for balance, and makes little logical sense.
That all said, I'm highly pessimistic about removing this feature. Credits to the balance team for all the great work they've done thus far, but this would require a complete rework of the entire underwater balance. That to me sounds like an enormous task, and I'm afraid of having another firebeetle situation where we have a unit that no-one knows what to do with.
I'm not convinced such a task would be a wise use of the balance team's time, nor that the final result is ensured to be a net benefit to the game.