upgrades do work but there are only a few.
And why would they give you a brand new salmon? They weren't even being produced anymore at the time.
Same for the Gato, why would you be given a new gato which is essentially exactly the same as the one you've currently got?
If you're asked if you want a new boat that's exactly what you'll get. If you want to get upgrades, just turn down the offer and wait a few patrols. After a specific date - 1942/07/01 for the Salmon - a message will come up (in port) saying your conning tower was upgraded.
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