If I apply points to a CDJapan purchase, will the billing information on my package show the original price without the points being applied, or will it show the price of where the points have been reduced?
The package itself will always display the original pricing (so using points won't help avoid customs sadly), but the bill in the package itself shows the price minus the points deduction.
But your order confirmation will show the reduced price! So when you make the customs declaration, you can subtract the points you used from the total.