"The name Nebuchadnezzar is most likely a reference to the palace where Alexander the Great died. Alexander was similar to Neo as he was raised and considered as the One and Neo also died in the Nebuchadnezzar."
Edit summary: "The reference was most likely wrongly attributed to the man which the palace was named."
I think the Wachowskis have said that they actually named this after the giant bottles of wine of the same name... but this is much better! The Wikipedia article does confirm that he died there, which was also news to me... so thanks mysterious IP editor!