They are painted on. One of the great things about Japanese planes is the markings. I have an Olfa circle cutter and I got some sheets of kabuki tape. Measure out the diameter of the circles from the decals then divide by 2. Adjust the olfa circle cutter and away you go.
Actually - its the placement of the mask that is the tricky part!
Make sure to spray straight down on the mask so you minimize the chance of any paint creep!