Vote #1 Amy Dakin: Amy Dakin’s answer to Ancient Greek transliteration: why does the letter κ become c, and the letter υ become y?
Bear in mind that K was imported into Latin from Greek, but it was a something of an affectation. It was never used seriously, so it was never going to be used in the latinization of Greek.
The reason Upsilon was imported into Latin from Greek was that Upsilon by then really did have a distinct sound from I and U. In fact we know that Upsilon was pronounced as ü in Greek right up until the 11th century.
Vote #1 Amy Dakin.