You will probably get better answers by posting in the Help With Repairs forum. I'm not sure that I exactly understand all of your questions, but here goes.....
The upper plugs are there to keep water from getting into the hulls, period. If they are leaking, they should be replaced/sealed, except......The holes in the front pylon plugs had tubes in them at one time. These tubes aren't for drainage, but for hull ventilation, so don't seal them. (Along with removal of the transom drain plugs, this is all the hull ventilation there is on a stock H16.) Any water on top of these plugs is of no concern, and very little if any water can get into the hulls through the vent tubes during normal operation. If you have water getting into your hulls, search for bubble leak test in the Help With Repairs forum. These pix may also help....
https://www.thebeachcats.com/pictures?g ... 5a21aacfb0The "plugs" at the pylon base are actually pylon shoes that are glassed into the inside of the keels. See the last two pix linked above, These shoes are structural and have nothing to do with drainage.
Hope this helps!