This is an interesting question. I've never thought the duck trouser detail was anything more than Stephen Crane putting in a specific, real detail. Duck cloth is a heavy, plain-woven cotton fabric. It's sometimes used for art canvases because of its stiff, durable nature. It makes sense that Crane points out that kind of clothing detail. Those pants are cheap to produce and durable. The material is also advantageous in a number of ways for artillerymen. The material isn't prone to snagging or tearing, and those men are constantly pushing and pulling heavy metal and wood around to fire their pieces. Duck cloth is also excellent at blocking wind. These soldiers are up on hills and ridges that overlook battlefields.

On the top of the hill a battery was arguing in tremendous roars with some other guns and to the eye of the infantry, the artillerymen, the guns, the caissons, the horses, were distinctly outlined upon the blue sky.

That location is likely to be one of the colder and windier locations on the field of battle. Finally, duck cloth is a bit burn resistant. Small sparks and hot ash won't ruin the fabric. The guns are Civil War pieces. The powder charge is packed down the gun separate from the round. Then an external fuse is used to light the powder charge. The flammable and explosive materials are not kept inside the rounds themselves. Sparks and fire are part the job and a real hazard, so for me, the duck pants detail is emphasized by Crane to give his short story even more realism.