The brown ones were only during the very beginning, the SA also had brown uniforms. Later the SS become more distinct from the SA and adopted their new uniforms, then the SA was destroyed because the SS was better. Anyways, enough history lessons.
But the SS is actually wearing black in Wolfenstein 3d, it's just the palette doesn't have enough shades of gray, so they used blue.
It kind of like how comic books do, like this: