I need to remove the side stay/shroud tag on a miracle 20 and I need to know if the nutsts on the inside are going to fall off into the bottom (inside) of the boat or if they are embedded in the Glass layup. Can someone enlighten me on this?

I don't know the answer to your question, but you may want to post it on the Hobie forum. The Hobie techs monitor that forum and tend to reply pretty quickly in most cases. They would be able to give you a definite answer.

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On mine the nuts were locknuts with the nylon insert, I wouldn't say they were glassed in, more like glassed over. If you succeed in getting the fasteners out without the nut turning, good luck getting the fasteners back in without the nuts turning.....

I installed a 4" inspection port on mine simple enough. Stay at least 2" away from the trunk lip as there is additional material around it on the inside.