The problem:
And yeah, fuel cost of "garbage ball" fleets (as they're affectionately known internally) are definitely at odds with the rest of industry encouraging exploration, which did come up in testing as well, but no obvious/clean solution presented itself.
A possible solution; it needs two components to work:
1) The hullmod "Monofilament tow cable"*, equippable on all ships. It enables to
tow one mothballed ship of the same size or smaller than the towing ship (or maybe one size bigger?).
Towed ships do not consume fuel in hyperspace. As a secondary effect a fleet can emergency burn even with a mothballed ship, when that ship is towed.
The hullmod could increase fuel consumption a bit, but I'm not sure if that would even be necessary balance-wise.
2) A skill in the Industry aptitude that enables to
restore mothballed ships with some of their CR. Maybe half of what they had before mothballing, but at least 40% (as long as the ship didn't have below 40%).
The hullmod and skill in combination would allow you to move a fleet for basically half the fuel cost (or less, when smaller ships can tow bigger ones), provided half of the ship tow, and half are towed. Then, when you got where you wanted, you restore the mothballed ships to re-acquire your full combat potential. Raising the CR again would of course cost many supplies, so you trade savings in fuel for restoration supply costs and intermittent vulnerability. Here D-hulls have an advantage, because it's much cheaper to restore them to full combat readiness.
That does not just enable to make far journeys with d-hull garbage fleets. It also opens other possibilities, like having a mothballed toolbox of highly specialized ships that you can restore when needed and carry around for cheap ( they don't cost fuel
and don't cost maintenance supply, after all). Or as a new option when you're stranded with low fuel in a remote system. As a nice side effect it gives more use for transports/liners, since you have to carry the crew for the mothballed ships somehow.
There are some ships were the tow cable might make for a nice build-in mod, like the Hound (sled dog!), the Venture and maybe even the tug (with then has a double function).
BTW, something that would be good regardless of if these ideas get implemented is an additional piece of information when hovering over the "mothball" button: "Restoring current CR after mothballing this ship will approximately cost x supplies". At the moment there is no warning at all that mothballing is costly.
*
Spoiler
From what I understand 8.1 will replace the tug's mono-filament tow cable with a "drive field stabilizer" that raises the entire fleets burn speed by 1, and the tow cable will not have any use.