The penetration of a 16" shell is tremendous. A true 'bunkerbuster'.
Not many bombs have the capability of them.
At Iwo Jima we bombed the Japanese pillboxes with little results. Location of some of the pillboxes in the side of Mt. Surabachi also negated the effectiveness of bombs. It was 16" shells from battleships offshore that penetrated and neutralize them.
I know we have penetrator bombs but don't know whether they are as effective as a 16" shell.
The heaviest bomb carried by Navy/Marine aircraft was probably a 500-lb GP bomb. It would have been delivered in a shallow dive -- probably not very accurate when you're trying to hit a cave entrance (nor would it penetrate all that far as you said). Todays aircraft delivered weapons would tend to be a lot more accurate and penetrate much further.
A GPS thousand pound bomb going through the airvent or door or window somewhere around the speed of sound will do more than a 16" shell ever thought about.
But as said before, a battleship sitting just on the edge of the horizon would be a scary ass thing to see.
But then, just blowing up without seeing what hit you (say a hellfire from a loitering predator) is pretty darn scary, too.