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For the Coral Sea historical take on it, Shouhou was to provide air cover for the invasion forces intended to take Port Moresby. Shoukaku and Zuikaku were there to enage any enemy vessel that happened along.
As for the flight decks...Akagi and Hiryuu had their bridge superstructures (island) on the left (port) side of the flight decks. All the other ships in the world (that had islands) had them on the right (starboard) side of the flight decks. Since the art for the shipgirls of these two ships have their decks on opposite arms, this is not the reason. This is more likely so that the two girls in the pair can be side by side without either blocking the other's deck.
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