If it stacks then won't there be some trouble using the ability? or does clicking on the stack use it for the whole stack on one target?
The ability triggers once per stack not once per pillar.
The stacking is a disadvantage to balance the effect.
So if you click a stack of 2 Black Obelisks it will drain 1 life from the target.
However the stack would produce 2
per turn.
These are meant to augment an existing quanta base.