I think this might be the same case with the Typ II and how many torpedoes it would carry. Theoretically it was 6, but most war patrols were carried out with 5, since the only place available to put the 6th, it was above the hatch to the battery area, virtually blocking it, IIRC.
Maybe this is a similar case with the IXD/2. It's a big fat sub. If you really needed more torpedos there should ve been space to put them. It just probably wasn't practical for the "average" war patrol, whatever average means.
Actually I like the IXD/2 better than the IXB,C. Feels safer (isn't actually) and has more torps.
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