No answers for you, but I've noticed the same thing. Most of them are good, like increased torpedo speed or increased submerged speed. I would assume that the idea behind this is that someone who was really really good at what they did could improve various areas of ship performance. I would also assume these are good because their icons are colored green.
On a scarier, stranger note, I noticed one of my watch officers had a red command icon that said "Global Ability: Increased Fanatical Chance." What in the world does that mean, and is it a bad thing? If so, as soon as I get back to Brisbane, he's getting dismissed.
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