Daniel, we are replacing the 2 marine heads on our WS42 ketch with 2 Nature's Heads.  I'd enjoy chatting about your decision and thought process sometime.

However, your question was about the what to do with the through hull and their obligatory holes.  Since we had to eliminate 4 through hulls, a good thing, we've had to cross this bridge.  We have glassed over the holes with fiberglass and epoxy.  I look at it as a 2 part process:  the inside of the hull and the outside of the hull.  However, the key here is to ensure that the fiberblass "patch" is large enough to create a good sized bonding area and thick enough to be strong enough.

To do the inside, we put Gorilla tape over the hole in the hull, filled the hole with West System Gap Filler, and layered several layers of cloth and epoxy over the area.  Once that cures, we did the outside.

To do the outside it is important to remember that the hull needs to be smooth.  One could just layer a bunch of fiberglass with epoxy over the area, but it would look like He** and not work optimally!  The outside process is more involved because you have to grind out a concave area into which you will layer cloth and epoxy.  Once the lay-up is done and cured, it must be sanded and faired with epoxy fillers to match the hull.  I would recommend a barrier coat over the area for protection.

There are several You Tube videos on this under the title of patching a hole in the hull.

For me the worst part is pressing the trigger to start grinding the concave area.  The thoughts of messing up twists the stomach a bit, but once started it fairly straight forward.

I have done this on several boats and it is more nerve wracking than difficult.  Like you thought process on composting heads, I am available to chat about the heads and the patching.

Doug