Some reasons to use zero-ohm resistors:

Machine-installable.

Jumper replacement. It allows to enable or disable a signal just like a single jumper, also useful to select between different connections to a signal

DIP-switch replacement. Useful when you want permanent settings.

Jump a signal over the top of another trace, especially on 1-layer boards or congested boards.

Set an assembly build number when you install different parts on a PCB. One or more digital inputs would each have a choice of stuffing a resistor to either Gnd or Vlogic to make a 0/1 logic value, which allows a processor to read it so it will know which hardware is installed on the PCB.

Alternate for current measurement resistor on a power rail. It's helpful to add a resistor after a voltage regulator. During development, you can install a 0.1ohm (or other value) resistor for manual current measurements, then during production you can install a zero-ohm in the same location.

Isolate inputs or outputs between analog and digital circuits, by unsoldering resistor during development, servicing, or fix circuits. After removing the resistor, you can solder a wire to a pad to probe the output, or feed the input, also you could solder wires on both resistor pads to run wires to another circuit, so you can modify a signal.