It comes down to what's conveniently available on the PCB. On breadboard I'd just use internal pull up resistors so I don't need to deal with external resistors. The code will need to be set to account for any changes.
ie if the pull down is used with switch to 5v, the code runs when the pin goes high. If you changed to pull up resistors and switch to ground, the code would have to be changed to run when the pin goes low.
Simple to change either way.