I don't know if it's been fixed yet, but I played an Intermediate AI game on the first day the patch came out and none of the AI had the new Keystone Masteries. Either it was a glitch an they just weren't visible, or they actually weren't updated. I'm guessing it's the latter, but I'm not positive.
I remember the old AI supposedly did use Masteries/Runes, but these new ones are not doing it. I don't play many AI games anymore, but they are a decent place for learning how a champion's kit works. While the AI for this game is never going to be perfect, it should at least have the same basic aspects as a normal PVP match.