Anchored ships, especially in stock, will regenerate, either upon your next game start, or upon the next spawn cycle (which wildly varies). It is next to impossible to "eliminate" a ship as sunk-is-sunk in the game, without outside intervention. Besides "bases", there were also fueling stations, anchorages, etc. where you might find a ship anchored. There were four main naval districts, Maizuru on the west Coast, Sasebo (Nagasaki) on the West end, Kure (Inland Sea) and Yokosuka (Tokyo). However, just the Inland Sea itself probably held over a dozen "bases" and the submarine training school... You start adding in the Mandates and conquered territories after Feb 1942, and there are a lot of places that are "bases". I'd guess about 3 dozen or more. The game itself on the Fleet Boat side does not attempt to go beyond what you would find in the Jap_HarborTraffic.mis file in the Data / Campaigns / Campaign folder to simulate the "bases". Nothing is listed as a "base" in there, but you do see the "docked" ships that you found. That file would be different between different mods.
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