I wonder if a thru-hull that is NPS can be re-cut to NPT on the end since it is already the same thread pitch. I understand what you are pointing out; but many, many boats have ball valves installed onto the thru-hull and there are not lots of reports of boats sinking due to this type of installation.
With a thru-hull that is clamped to the hull via the retaining nut you have lesser chance of the fitting leaking and no extra fasteners penetrating the hull. If a flange mounted seacock leaks you need to pull the boat to fix the leak; with a retaining nut you can attempt to tighten it first. If the thru-hull fitting had NPT re-cut on the end it would be better than a flanged secock (I think).
Actually approximately 50% of boat sinking's are as a result of failed below water fittings and a good chunk of this 50% is directly related to failed through hulls or valves as well as hose clamps and hoses. Boats do sink because of improper through hull configurations. A neighbor of mine lost his boat in a lightning strike right in front of our house. Why? Because the few threads holding his gate valve onto his through hull gave way when the current tried to find it's way back to the water. The valve blew right off the through hull. His insurance company tried to decline coverage because the valve was not a marine rated valve and not a proper ABYC or industry installation of a proper seacock. He got a lawyer, fought it and won. The only reason he won was because they had not requested he install proper ABYC or industry accepted seacocks when they examined his initial survey from when he bought the boat..
On my most recent boat purchase (CS-36) my insurance company (Amica) made me replace all my through-hull's w/valves with marine rated seacocks. They did not require, however, that they be through bolted but did require flanges and marine rated. After I installed them, and changed a bunch of other stuff they requested too, such as standing rigging, the surveyor had to come back and sign off. It's getting tougher and tougher to insure an older boat and they are mandating ABYC spec on many items...!
I personally had an improperly installed through hull crack on me when a heavy item under the sink, a spare alternator, fell & hit the valve in rough weather. My boat did not sink and I found the problem in time, thank god for bilge alarms, but I could have lost it.
There is a reason I'm passionate about this subject and it's because I've personally seen the consequences..
P.S. You can have NPS threads cut to what's called a "combination thread" and while still not NPT they are better than stuffing an NPS into an NPT fitting. You will incur machine shop expense or have to custom order the fittings pre-machined that way though and still not have the benefit of the strength of a flanged seacock.