For what reasons might someone choose a HULL D over the more maneuverable HULL C or the much more massive HULL E?

The simple answer is that the entire lineup is a sliding scale: as more and more cargo space is added, the speed and maneuverability is compromised. The Hull D is for pilots who want to move a lot of cargo, but aren't willing to go quite as slowly and methodically as the Hull E will require. While it's tempting to pick the highest number and decide that's the best, it's likely that most independent captains would get more bang for their buck with a smaller ship fully laden rather than struggling to afford as much cargo as it would take to stock a Hull E.