surely the best way is just to increase the inaccuracy of depth charges, but make them rely on blast radius to do damage? In fact, AFAIK with the new version of spring we have the opportunity to make depth charges a lot more like they were in real life (which while on its own is not essential, would be good for game balance in this case).
EG you could make depth charges into ballistic weapons launched through the air that when hitting the water, fire off another projectile (same graphic) that drifts downwards and explodes with a reasonable radius at typical submarine depth.
Both 'weapons' would look like a depth charge, its just a way of getting around the water barrier.