#1 reason, replacing things. Very regularly lights, blinkers and switches are broken or missing. Of the past 5 bikes only 1 had a complete set of working switches, and on 2 a faulty switch was a part of their problem. Then factor in new controls, new switches means often the old wiring doesnt work - a common one is NC to NO brake switches for example.
Going to a whole new ignition often means a rather drastic rearrangement.
#1.5 Customizing a bike people regularly use custom lights, many times single filament instead of the stock dual beam front and brake/tail rear.
#2, bikes with the taillight ground, best to avoid that potential for a problem
Combine any of those reasons and factor in simplicity (and laziness) - in all these cases it's by far simplest to start from scratch, omit potential for unseen faults and just go power to headlight an taillight, ignition to coil, and a simple kill switch or button. 3 wires and you have a ridable bike vs digging through a pile of spaghetti behind the headlight bucket with a multimeter and a wiring diagram trying to figure out which wire's orange and which ones are just faded red and why don't they have power when flipping the switch and I dont want to pay $15 and wait a week for a new switch so fuckit - hardwire