Cross posting from Reddit. I was able to purchase points but I had to have someone with access to online credit card transactions on the phone to change the security settings on my card as well as monitor the transaction. Even with a successful transaction, the error message appeared for a few seconds.

Also I did see the "Verified by Visa" window during my transactions but I did not have to enter a password. I believe results will vary by credit card issuer and the generic information Visa provides may not be accurate. The software of the credit card issuer must be able to work with that of Nico Nico.

PS - Contacted credit card issuer about Mastercard Securecode. They had no idea what that was.