All of that, i.e. where you can ship out from, depend on the class of boat, and the date. All of the boats were assigned in Submarine Squadrons, SubRon's for short. They mostly kept like boats together. When the Gato class was first available, it was first sent to Pearl based SubRon's due to it's range and stronger hulls for Empire patrols. The Gato's replaced older boats as need be, so they were slower to reach SUBSOWESPAC squadrons as compared to Pearl.
So, this is implemented in game by each class of boat showing up as available at different bases at different times in the Campaign as compared to what boats were in service where and when historically.
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