I think I've figured it out. It doesn't give you the option to deploy or pick up anything until you surface at the destination. Discovered this when I had to drop some troops off in the Philippines - I made it to my destination at around 00:30, but I was already surfaced. I waited around, nothing.... Then just for ****s and giggles, I thought, "What happens if I submerge and then surface?" Sure enough, as soon as my deck watch was on duty, a box came up. A little pedantic maybe, but I think this operation of the game was designed with the thought that subs would stay submerged as long as possible and surface only long enough to deploy/pick up at the destination, then submerge again. Moral of the story - stay under until you've reached the destination, then pop up and you should be able to complete your mission by sending out rafts, picking up pilots, etc.
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