Wayne,
First and foremost, it's 80 years after the course was built so land shifting and settling is to be expected. No architect - well other than Tom Doak - could foresee that.
Second of all, and I'm taking the golf course superintendent on his word with this, the sea level has risen in the last 15 years. For instance, the land had to be raised on the right side of the 16th green because unusually high tides - not storm surges - were getting into the bunker. The land does not show signs of settling.
If you have not seen a lake or pond on the land then you did not look hard enough. Mr. Fay was right in his description. Fresh water ponds can be found on 1, 2, 4, 7, 8, and 17. Originally the pond on 1 went well into the fairway.
I cannot even attempt to act as if I know what a long-deceased architect was thinking but I do know this, if I was building the golf course now and was allowed, I'd route the holes in the corridors that are 12, 13, and 14 without hesitation. Yes, there might be salt water contamination problems but I would be a fool not to take the golfer right to the ocean as often as I could.
And who knows, maybe the course did drain better 80 years ago. The salt water inlet next to 13 and 14 may have been much deeper and therefore capable of handling the higher tides better. For all we know there could be sediment 6 feet deep that wasn't there.
Just because it is the way it is now, does not mean that is how it always was or will be.
Not sure what you mean by "The remediation efforts that cost so much money to fix the problem corrected the problem."
Anthony