Hogans Alley is just a place to store crew. Basically made to deal with a bug that can't be fixed. If you leave your men on deck or AA guns while dived the game still see's them outside of the sub, so a charge easily kills them. It doesn't harm a thing to fill it up if you want.
For sure while in port look at the stat numbers, why not get the highest rating men you can and trade them out. They're some good mechs in port.
I go ahead and fill my damage crew compartment why at port, then fill the alley except for a few spots so I can move men around.
Just drag them over to the left where the men are why in port to get rid of them, same as you drag men to your boat.
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