If you aren't trying to save the dot, you could just drill it out with a smaller bit. If you tapped it with a center punch, it would probably break & chip out. If you want to save it, try glueing a dowel rod to the dot, then pull it up & out. I have used a small exacto knife to pry them out but it usually chips the edge of the pearl dot. I had removed the neck on an old National mando and the dots covered up the screws on the fingerboard extension. My Daley has a blank fingerboard as the previous owner had ordered it that way. I don't miss them.
Cabin Fever String Band, National Pike Pickers