FWIW, a British N class destroyer would have been about 110 m long and 11 m wide, while a German Type VII sub would have been 67 m long and 6 m wide... The respective displacements would have been 2,300 tons and 870 tons (submerged).
If we ignore nacelles and pylons (or scale them in terms of the respective propulsive performances of the destroyer and the sub, rather than size), option 2 is probably the closest to the WWII comparison: the primary hulls are in similar length and height relationship to each other then. But a submarine's hull is usable to a much smaller degree than a destroyer's: the pressure hull is smaller than the overall hull, and there's no useful superstructure. In that sense, option 1 would be closer - and the difference in nacelle size would truly begin to approximate the propulsive disparity between a destroyer and a sub!
The displacement ratio would probably favor something between options 1 and 2...