I have seen them leak between the plexiglass and the hatch many times as well. Usually though the dogs in the plexiglass keep that pressured down...
5200 bonds and stays put when the surface is prepped correctly (so does 4200 but it's just not as strong of a bond), there shouldn't be that much...
Given what you've said, I'd pull your deck hatches and re-seal them to. I had a Cabo 35' many years ago, had a leak up there when the owner ran...
I like kvh products and haven’t had any issues with them.