Clunking noise in front end of harley

Would guess that they are not bottoming out, they are topping out. doubt that you get them to full compression on bumps or braking would really be a bad experience, it's more likely that after compression on a bump, the forks spring back out as far as they will go and reach the end of their travel, it's because they aren't very sporty forks and lack enough rebound damping. I have a 2008 1200 sportster and it does it. cure would be maybe thicker oil in forks to slow up the rebound but would also slow the up stroke over bumps. you can get just about evey accessory for a Harley so there's probably a kit available to fix the damping.