Are you saying these through hulls are just that with ball valves and not true seacocks?
If true seacocks, why do anything other than leave shut with the top plugged or with a piece of hose thats plugged.
If you have ball valves screwed onto through hulls and you are going through the effort to remove them, I would just epoxy up the holes correctly and be done with it. Nothing else is really safer unless you install a real seacock.
By the time you want an overboard discharge directly from the toilets which isvwhat I am guessing you have, hardly anyone has a system set up like that anyway these days of type 1s and the growing number of no discharge areas.
They're seacocks, which are blocked at the discharge end. The boat originally had three discharge holes...one for the single holding tank macerator, and one each for the two heads. There were/are also seacocks for the raw water flush intakes. All are currently closed and the output openings are plugged and clamped. The heads are now fresh water flush and discharge directly into the original forward(common) holding tank and the new aft holding tank.
I want to retain the aft opening in the event I or the next owner wants to plumb a macerator/overboard pump to the tank. Same for the original forward tank....retain option of a macerator pump, which was removed when I modified the system for Great Lakes operation. That leaves the forward direct head discharge, and the two raw water intakes. The forward water intake hole is in a good location for a second depth finder, so I want to retain it.
So, two holes could be glassed over, I suppose. Three might have future application. The boat comes out of the water every year, so I have annual access. I was thinking a solid plug in the three "future use" holes would be more safe than the seacocks with plugs.
Anyway, I now have some great advice and will make a plan. By the way, I just completed a
self survey for my 5-6 year insurance renewal, and they asked that a wooden plug kit be on board in the event of a leaking seacock. This is what got me thinking about "hardening" the thru-hull setup. By the way, my insurance company is Markel, and they are to be applauded for moving toward self surveys. Y'all might want to suggest to your company to eliminate the "surveyor" tax. In this age of digital photos, it is quite ridiculous. (Or switch to Markel).