The correct answer should be as few as possible. At 3am when the water is gently lapping over the deck boards the less places you have to check the better. Having to check 13 sea cocks (I was wrong in my previous post, I found another one), four transducer/speed log fittings and the sonar from hell, might get a little tiresome. Therefore nine holes were destined to be ground out and filled in. The removal is the fun part (except for the fiberglass dust) as I was always good at taking things apart.
The patching of the holes is a whole other matter.