It deals "damage" to AP. Really useful if an opponent has lots of AP, but doesn't hit hard with regular physical attacks (e.g. mages). Even at Lvl. 10 (easy enough to level it to), it will usually drain an enemy's AP to 0 in one hit. The "12%" must refer to how much "damage" it does. So, if your regular attack does 1,000 HP damage, Manastrike will drop the enemy's AP by 120.
It seems it deals damage towards ap and not hp. I burned away killimg machine's whole ap with one hit.