Actually the Barb and the Tirante both infiltrated heavily defended enemy anchorages at night and wreaked havoc among the anchored Japanese convoys there, so doing so was certainly possible. That it wasn't done a lot probably has more to do with the subs primary mission being interdicting commercial shipping.
It's too easy to do so in SH4, but this is much due to the AI and the fact the game is obviously designed around approaches only. But the point remains that if someone should have the guts to try (and succeed) such a strike should have a major impact on how the rest of the campaign plays out.
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