You know, reading over this thread, I've got an idea for a scene that should be in the movie to explain the zero in the registry.
Exterior Kelvin hull. Workers are welding the ship together, similar to the Enterprise being welded in the trailer. Among the welders is a main painting on the hull. He has already painted NCC and is finishing the dash. At this moment, badass techno-disco music plays as the Badass Captain Robau struts out onto the hull. His uniform shirt is open half-way down his chest, because he is badass.
Robau: "I want this ship to have a four digit registry."
Painter: "I'm sorry sir, that's not possible. The ship's registry is NCC-514. That's only a three-digit number."
Robau: "Then put a zero in front of the registry."
Painter: "Sir?"
Robau: "Make the registry NCC-0514."
Painter: "I don't think I can do-"
Robau: "I am the Badass Captain Robau! If I want a four digit registry for my ship, then I will have a four-digit registry for my ship. Now paint me a zero."
Sighing, the painter paints 0514 until the hull.
Robau: "Badass."
Badass techno-disco music plays as Robau struts away.