Norzoh'thelax
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From the APG "Communing with [her patron], using her familiar as a conduit, the witch gains not only a host of spells but a number of strange abilities known as hexes." In addition, also from the APG, all of the hexes are listed as supernatural abilities i.e. Fortune(Su), Blight(Su), etc...
The bestiary says "The following feats apply specifically to monsters although some PC's may qualify for them." - in other words it allows PC's to use the feats they qualify for, while noting that many of the abilities will be more monster accessible/useful.
In the bestiary creature listings Ability Focus is coupled with a variety of supernatural abilities like Charming Gaze(Su), Roar(Su), Confusion(Su), and Rust(Su) which are similar in usage to hexes - standard actions which do not provoke attacks of opportunity.
So, I would rule that clearly Ability Focus was meant for use with supernatural abilities but that each Hex is a separate ability (each hex tracks its use against each enemy separately).
Outside of the primary vein of this thread, I think the main issue with Hexes for GM's are things like Slumber's lack of hit die restriction. The trick is have your bad guys wake each other up. Then the hex is used up and combat can move on.
One Important Caveat: In society play - Feats from the Bestiary are NOT legal for PC's, familiar's, or animal companions unless specifically granted by another legal source.