Against an AP mid you don't need the armor and the health is useful for staying alive. Scaling health is more beneficial than flat health if you can survive well early game, which Ahri can, but around the mid game you should start to roam more, and you'll be getting more benefit out of scaling health in the midgame than you would out of flat hp runes. More HP also works fairly well with Ahri's passive, so you can heal up even more.
If you're against an AD mid, take armor seals pretty much every time. Mana regen seals are kind of a waste once you get morellos/chalice/blue buff so there's no point in running them. You do use a lot of mana early, but the key is to conserve mana until you get your mana regen item, so that means you're mostly going to be aa'ing to farm with an occasional Q to clear a wave (and hopefully harass your opponent at the same time). Don't be afraid to use your full combo if you're sure you can land the charm though, it's well worth pushing your opponent out of lane for a little while.