I'm unsure if the dmg calc has been updated but pre-patch throwing hammers were on par with regular throwing axes on heavily armored targets (50+ armor). Not to mention they're quite a bit cheaper than heavy axes. Its generally best to bring a stack of each, unless the enemy team is stacking a certain type of armor (lots of lights or lights of heavies)
Save hammers & pierce for medium+ armored targets, use axes vs unarmored targets and light horses.
Axes are however great for headshotting people who skimp on head armor but use heavy body armor.