I've often thought of bedding deck hardware on the bare glass, in thickened epoxy, with no mechanical fasteners. This would require judicious use of clamps and perhaps powerful magnets, but I am reasonably confident it would work. This would create no leak worries, and only require a bit of paint around the fitting base. That is, unless you glue to the gelcoat, which would probably work just as well.
I would definitely not try this on a mooring cleat, but it could be just the ticket for little non critical deck hardware!