It's probably just an error - someone didn't check carefully enough. The boat does dive and there's still many abilities that crew members have that work properly at 0 morale. But a) why some things like guns don't; b) why the game just drops morale like that - that is definitely puzzling. Patch priority #1 if there ever was any. The fix shouldn't be difficult.
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There are only forty people in the world and five of them are hamburgers.
-Don Van Vliet (aka Captain Beefheart)
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