Anyone have a better way to tie this? so it is more secure, and maybe without a massive knot in the way? or something that just looks cleaner.

I understand you want very much to stay with this particular nunchaku, right?
I would take of all metallic parts except the cover, then instead of bearing placed sick plastic disk with the hole in the center, made a loop with the rope and hided the knot inside of the metallic cover behind plastic disk.
if you want the drawing just send me in private your email. I still have no permissions or something to post images here...