I'm guessing that either they were in negotiations for a potential renewal / extension to the license or (far more likely) they didn't want headlines about their feud with Google taking attention away from the product announcement.
They never mentioned YouTube on stage though, it just wasn't yet removed from the developer previews. That's like saying Apple advertised Mountain Lion as having the 32-bit kernel because it was present in DP1.
I have little doubt they were planning to remove it the entire time and it just wasn't a high priority issue until the license expired in between beta 3 and beta 4.
