The bolts are threaded into a piece of SS or AL that is glassed into the deck as shown on the first page. Are you able to reach the undersides of your bolts through deck hatches?

Your drill going out the bottom of the bolt can be a problem, but you should not hit glass. If you have not already, start soaking them in a penetrant oil. Because the bolts are seized, your gonna have a really hard time using any sort of extractor until you do something to make the bolts loosen up. Heat and PB blaster normally do the trick for me, but heat is not a option for you.

I would use a cobalt drill bit, keep it REALLY lubricated and very centered and keep working up in size until your just slightly smaller than the minor diameter of the threads. Then something like a scribe can make short work of getting the threads out. Normally I do this on a mill and it works great.