Its probably worthwhile to cut open one of the smaller bubbles and find out what's inside it. I've seen bubbles develop when a poorly mixed batch of epoxy during the wetting-out stage didn't cure, but got covered over by subsequent coats. Everything looked fine until it was exposed to the sun. Then the uncured areas delaminated, leaving bubbles of semi-cured epoxy.

I can't see why you should be getting water bubbles unless there is also delamination. Even if you drilled a hole through your boat the glass shouldn't separate from the wood until the wood is weakened severly by the water damage.