Smitty, While I do not condone working on a boat without opening your beer (cap is still on it in the top pics...LOL), I think I know what is going on with your cans.
While I am not sure about your specific questions, I do think I know where the holes came (since I have Skylon speakers as well).
Go to the bottom of this webpage and you will see the lights that go to those cans and that is what it looks like the hole in your 3rd picture may have been for: http://www.skylonsports.com/products/lightsmirrors.php
Hope that helps in some way....maybe you should just put your speakers in and order a new set of lights to plug those holes????