The ship has all the same mission specific design elements as any other ship. The only difference is that any space that used to be fuel only is now capable of carrying 95% of the volume as cargo if no fuel is needed.
The ship AnotherDilbert listed has J3 with drop tank in tow. This would allow 35 000 tons of additional cargo to be brought along. The merits and risks of any weapons being transported in a cargo bay as opposed to an explosion proof magazines is another topic, but the ability to carry something useful when fuel is not needed is something to look at.
For supply ships this is an obvious win, as with cargo ships of all sizes. Anytime you do not need a full load of fuel, take something along that pays the bills.
Let's look at a ship to see what it might miss.
Atlantic class Heavy Cruiser from highguard. pg 196
75000 tons Jump 4
30 000 tons of fuel needed for the Jump 4, 860 tons of fuel needed for 8 weeks operation.
The ship has 1174 tons of cargo space
Lets leave the 860 tons alone, and a J2 normal tank because Jump 2 is a conservative safety net.
If we converted the fuel tank area into cargo space and installed fuel/cargo containers we would need 750 tons of space from the 1174 tons of cargo space to accomodate this design. Yes, this would mean shuffling things around on the deckplan, or a redesign of the ship. The cruiser would lose a lot of cargo capacity during Jump 4 operations. 1174-750= 424 tons remaing, a big loss I admit. (Jump 3 tankage would only leave 50 tons of cargo)
This is a point against the tankage. At maximum output you lose the extra 5% of space, and that can be a problem.
Where the advantage can appear is when the ship is not jumping 4 hexes. If the ship only needs to Jump 3, it can carry an additional 7500 tons of cargo, 15000 tons if it only has to go Jump 2. In a pinch this heavy cruiser could carry 180 000 missiles into a system to help supply a fleet. That's not bad.
If you wanted to save the cargo space you could make the Jump 4 engines TL 13 and make them 5% more fuel eficient and then you leave the cargo space alone and the 15000 tons of fuel tankage holds all the fuel and piping needed. That would raise the cost of the ship by a billion credits for the Jump Drives, and the 15 000 tons of tankage costs 75 million.
This may be too expensive for the times a warship needs to carry cargo, but it does offer some interesting options.