I don't argue that unrefined ore would have less mass and volume than refined ore. However, there are no indication that what is mined could not also be refined at the same time. So what is shipped could actually be in its refined and pure form (Sorium being the only one we know is not refined).
With that said a construction of Duranium such as infrastructure could certainly have allot more volume than the unrefined Duranium ore, it could be several factors bigger in volume.
In my opinion you can't really know for sure what is what and ships mass is actually not its mass more it's size just noted in mass for convenience since that is a classic way of classify naval vessels in reality. Although speed and fuel usage is then calculated from it's size not its actual weight which become a little weird.
I think it would be a more legitimate question to ask why a cargo ship (or ships with hangars) require as much fuel when fully loaded as when empty. This goes for it's speed as well. The same with missile space, fuel etc.. It works for tugs.
I don't mind the simplicity as it is, but I would not mind that both volume and mass was used as well as different fuel and speed depending in the ordnance, cargo, fuel and flights carried by a ship.