Again I personally would never install NPS to NPS below the water line, with out some orther means of sealing like a proper flanged / bolted seacock but some do and feel comfortable with it..
I'm one of those on a limited basis. I wrote a whole blog piece, complete with illlustrations of threads, on why it was a bad idea and the yard service manager then said he had been replacing gate valves with NTP ball valves on NPS through hulls for 20 years and never heard of a problem. I put a trial fitting on one of the through hulls I took out and determined that the threads are closer and the material more flexible than you would think.
I never heard myself of tape and dope together but there is a lot of difference between domestic water pressure and hammer and the low pressure of most through hulls.
I would NOT use ball valves on through hulls anywhere were heavy items stored or someone's foot could hit them or on large diameter fittings like cockpit scuppers. I have just three thru hulls in my boat. Two are ball valves on old through hulls and they are under the head sink and small diameter.
I went to a lot of trouble to reduce the number of seacocks in my boat. I'm also more comfortable with simply capping unused through hulls with bronze caps than pulling them out and having a large fiberglass structural repairs with secondary bonds.
You can see how I got rid of my cockpit drain seacocks here:
http://home.roadrunner.com/~rlma/Strider.htm
All hotel drains go to the bilge sump on my boat and are then pumped overboard from there. I do not believe in trying to drain stuff below water level by gravity. Any floating stuff that goes down ends up floating as a little raft at the salt water level and then picking up more stuff until you have a clog. These are the kinds of drains that are also often on places you may forget to think about when you see water over the floorboards.