It would not apply for agent buildings, because as far as I know, you can only have those buildings in the province capital. I may be wrong though, I have not played Barbarian factions enough but for Greco-Roman factions, you can only have one of them. You can however spam temples and the bonuses do stack as far as I know. I don't know if they have changed this yet but I used this to my advantage when I gave the Scythians a try and made horse archers with huge amount of ammo.