Wasn't V'Ger damaged when the alien machine planet found it? It must have reconstructed the programming from what was left, and not knowing any better, taking every found detail literally.
If all the aliens saw was V___GER, and the probe couldn't tell them any different, why wouldn't they assume that was the probe's name?
The same questions get asked of those alien machines on the machine planet, then.
How would they even know that the marks on the probe's surface were letters to be read in the first place, much less that those letters would designate its name?
How is it that they happened to read the letters in the proper order, with the proper orientation?
If you can get all that right, then why don't you wonder about the ridiculously huge spacing between the V and the G, inappropriate for that font, and the muck on the surface in that space?