I had the same problem on a anchor locker hatch. I brought it to fiberglass guy. He opened the entire thing, replaced the wood core with structural foam, then re-glassed the entire thing. It was a few hundred bucks.
I wouldn't use silicone anywhere on a boat. 3M 4000 would be a better solution if you wanted to use a caulk. However, in such a high visibility area, that would not be aesthetically pleasing.
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