Im not sure I understand the full issue and how the nut got there to begin with, but just going on what i assume, if it were me, im pretty sure i would go with Chris's idea of scoring the deck around the bolt so the nut could be pulled out in a controlled manner, then glassing it over and re-drill the hole so you can install a backing plate and nuts from the inside... the organizer (or a larger bedding plate under it) will cover any ugly that is left behind on the deck, so a perfectly matching glass job is not mandatory.
but then on second thought, if the boat has a glass liner that is in the way, it is possible to gently cut a nice clean hole in the liner (a harbor freight vibrating multi-tool works great for this) so you can access the nuts between the coachroof and liner, then trim the cutout piece with either wood or some durable plastic to make a cover for the hole... and it will look nice.