I draw backgrounds by hand because it gives me tighter control on the composition of panels. I can place bits and pieces here and there with only a few lines and don't have to fiddle around with 3d programs so much.
However, using 3d programs is understandable if your art style is extremely detailed, or you're aiming for an aesthetic heavily rooted in realism.
Heck, the entirety of Kizumonogatari's backgrounds are 3d generated.