The numbers to the right of each crew member in your picture there are an indication of their 'rank'. Notice the drop-down selection box at the top of that list that says 'Rank'? You can select different attributes to sort the crew by from that list, such as 'Health' or 'Morale' or 'Skills'. You can also select a crew member from that list and the box around them will be highlighted where they're located in your sub.
About the missing crew slots for your deck guns; I'm not sure on this one, but do you definitely have both a fore and aft deck gun? You might try adding one from the sub config screen if not. (I'm not sure what the screen looks like if you don't have one of the guns, so it may still be a bug...)
nomad_delta
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