It's mainly for neatness and manufacturability. A zero ohm resistor (whether it is SMD or through-hole) is not only neater and more professional looking, it's also easier to automate the assembly process of a board using jumpers. If you are assembling a board by hand, it's also a lot faster because there are no wires to strip, the thicker leads are easier to form than stranded wire but thicker than most commonplace solid wire, so the end result is more consistent.
Also, some boards use them as permanent jumpers for configuring a board to different settings. Other designs might require pads originally intended for resistors to be shorted out instead of using a resistor value for whatever reason (design changes, certain features removed or bypassed, etc).
No different than using PCB traces vs wires, really. Neatness, consistency, and manufacturability.