The Deck Crew is vulnerable when you are submerged. Though you don't see them, they are still at their "duty stations" up top, holding their breath, anxiously awaiting your surfacing of the boat again... so if you expect an attack, move your deck crew to the Repair Crew section. As you mention, some of the mods do create a "Hogan's Alley", but you still have to drag the fellers by the hair over into those slots. Nothing can be done to "automate" it. You'll notice that if you take a depth charge near-miss, and you get the message "Periscope damaged sir!", you might also hear a cry "Medic!" (or even a SpongeBob "Muh ~LEG~!!!") and a couple of the fellers on the watch crew have either been wounded or killed. Similar happens to the gun crews if they were manned... Like that flag on the boat, nothing really "disappears" when you submerge, it just becomes "invisible" - but it's still there...
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