They don't. The D5 in "Marauders" was fitted out with huge fuel tanks and had one of its disruptor cannons removed.
It's also puzzling why some ships have a "D" class and others don't. The D4 patrol ships from STID certainly aren't related to the D5 cruisers we saw in the 22nd century, which leads me to wonder if the small ship that the Augments stole in the borderlands was a 22nd century D4. And then there's the Raptor class cruiser which looks more like the later Klingon ships than anything else we ever saw (D6?) and the big four-gun bird of prey that is somehow large enough to have its own shuttlebay (D2, mighty duck class?)
Indeed.
D5, D7, etc... could simply refer to the ship's platform or frame. Showing my age here, but think back to the Chryslers/Dodges of the 80s and early 90s. Nearly every car produced by the company was a K-car or built on a chassis derived from the K-platform. Many car manufactures still do this. GM has the Alpha, Delta, Epsilon and other platforms. Ford has the B, C and D platforms.
The vehicles that use these chassis look different enough from other vehicles using the same chassis.
Just my $0.02