Dana is describing approach of a rain storm, not far from the equator, and men having to take steps to keep rain from doing any harm. He mentions the "booby hatch" being closed.
"Booby" refers to a sea bird, easily caught on shore. And a term applied to stupid gullible people. "Booby hatch" is a farily common slang term for a mental hospital.
I'm unsure why the hatch should be so described. Do you know, Faldage?