A IX is best used away from convoys later in the war. Earlier in the war, it's fine against them. Also, it's only a few seconds slower in the dive than a VII. "dives as if the sea was fighting against her" is a gross exaggeration. If you really want, your extra fuel lets you run decks awash for the same range as a VII, and in that case, you can dive MUCH faster than a non-awash VII.
Besides that, the extra torps make a significant difference in your total tonnage, as does being able to get away from the North Atlantic to juicier areas (like Africa, Caribbean, or 1941 US). I'd go for the IX, unless you really like the North Atlantic convoy action.
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