The Arrow Of Harming doesn't deal more damage than the other arrows.

From my testing, regular arrows at full charge deal 6-10 damage. Arrows of Harming... also deal 6-10 damage. So it looks the potion effect isn't working at all, rather than only dealing a small amount of damage, probably due to invincibility time or conflict with the arrow damage. I tested damage using several command blocks and the scoreboard.

One command block summoned a villager for target practice:

/summon Villager 61 64 285 {CustomName:"Dummy"}

The scoreboard was set up with:

/scoreboard objectives add MH dummy Health
/scoreboard objectives setdisplay sidebar MH

The other command blocks each checked for a specific health value, and set Dummy's score to that value:

/scoreboard players set @e[type=Villager] MH 1 {CustomName:"Dummy", Health:1s}
/scoreboard players set @e[type=Villager] MH 2 {CustomName:"Dummy", Health:2s}
/scoreboard players set @e[type=Villager] MH 3 {CustomName:"Dummy", Health:3s}
...
/scoreboard players set @e[type=Villager] MH 20 {CustomName:"Dummy", Health:20s}

This is still present in Minecraft 1.10.

This bug also applies to Arrows of Healing.

Fixed in 16w32a

Seems like the same issue as MC-107856 (which mentions how either only the harming or the bow damage is being applied due to damage cooldown).