If I'm picking up my PADI AOW along with actually doing the specialties (PPB, Drift, Night), do I still pay full price for AOW or should it be discount? Or should I get discounts on the specialties?
Simple answer: every shop and instructor has their own pricing policy, so there is no universal policy that would apply to your situation.
Just seems odd to pay full price for each of them, even though I'm doing dives for the specialties on the AOW dives. Maybe I'm missing something obvious?
You're not missing something: as many people here have already responded, if the shop will try to "package" your specialties with your AOW (i.e. cut down on the total number of dives, and cut down on the work they have to do for you) then it is reasonable that you should be able to ask for an appropriate "package" price.