I imagine dive speed would be a big problem and you'd need an impractically big pair of engines to drive such a large vessel at any decent speed, and the underwater speed would be pretty bad too since this is the era before tear-drop hull shapes.
A design like the I-400s might work, but you'd need to build a lot of them and that would take precious German manufacturing away from other projects. Remember that Doenitz wanted 300 uboats (100 on patrol in combat areas, 100 in dock, 100 in transit), but by wars start he only had 26 at sea and didn't get 100 at sea until 1942.
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