Some supermods might change this, but the stock game campaign gives all the awards based on "renown". Completing a mission usually gives 300 renown points. Sinking a single ship gives 250 to 1000 renown points, so I generally ignore mission objectives and just sink enemy ships - which is what the submarine was actually designed for in the first place. Realistically COMSUBPAC couldn't object to failing to complete the assigned mission if the results contributed substantually to winning the war. The game reflects that since there's no penalty for ignoring the objectives for every patrol - high tonnage with mission incomplete gets the points, completing the mission with low tonnage will get you canned.
That said, when I go back to base and end patrol, the new patrol starts with a new objective, haven't seen any yet where they give you the same objective for the next patrol.
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