The drill and fill is rarely done by riggers of boats, or the factory in production boats. That, or perhaps more frequently, some solid core material, is placed where thru hulls, cleats, life lines stanchions etc are placed when the boat is laminated, either in very high end boats or in custom boats.
I have done this on a number of boats--but not always, and not in all fittings. Several boats I have done it on every fitting (including the Cal 46 we rebuilt), and a couple of the C Dorys I have owned.
Should it be done? Absolutely. Why is it not done? Costs. Every production boat is done on a "Cost vs benefit" basis. The manufacturer figure most folks will now own a boat more than 5 to 10 years (max warrantee), and then it is someone else's problem. There are a lot of things done in boats on this principle. There are also reasons that the C Dory keeps it value far better than a Bayliner or Sea Ray.
The reality is that you don't see C Dory's being ground up and used for insulation or put into a land fill--where you do many other fiberglass boats. There have been some older (and a few newer) boats which have had core problems. 90+ % were boats left out in the open, water accumulated, freeze/thaw cycles, holes in the core, which allowed water intrusion. There have also been a very few boats which had factory defects--and for the most part there was restitution...But that is true of all boats.
Occasionally there is a catastrophic cored hull failure. I have seen photos of several. Not all were balsa. Some were caused by improper manufacture--and some by hitting a rock, and not repairing a core intrusion. But I have also cited in the past, where I was on a balsa cored boat which hit a container at 8 knots in 8 foot seas. The balsa absorbed most of the shock--3/8" outer glass (the thickness of many solid laminate hulls) was fractured--and an uncored boat would have sunk. In this case, there was delamination of the inner 1/4" glass over about 12 sq feet, but no hull breech. This happened in the middle of a dark night in 50 knot winds off the coast of Mexico. The difference between finishing the race (in first place), and spending some time in a life raft, until rescue elements arrived--and the potential loss of life, as well as loss of a very expensive boat.