The core Pathfinder rules for settlement demographics are in the PRD. It includes information on the highest level of spellcasting available in a settlement of each size. For example, in a large town (2001-5000 people) you can buy up to a 5th level spell. Even in a 20 person thorp you can get 1st level spells. This speaks to a certain level of commonality. If you want to flesh out a whole population, the 3.5e settlement rules had more thorough coverage.
There are however more Golarion specific rules in the Inner Sea World Guide p.253. To quote James Jacobs, Creative Director at Paizo, on the intent of this section from the Paizo forums:
I've always resisted nailing down exact numbers like this for NPC class levels, since I feel that it unnecessarily restricts adventure and sourcebook writing on the hobbyist and professional levels. Because once it's in print, folks tend to treat those numbers as sacrosanct; it's what happened with D&D, and as a result lots of people felt it was cheating to do something like have a super high level NPC live in a small town... which was already canon for a lot of places (such as Elminster living in Shadowdale).
The information on this topic I put into the Inner Sea World Guide is on page 253. It doesn't have MUCH to say, but it does break class levels down into four bands:
Standard (1st–5th level): This is where the vast majority of people are. It's very VERY uncommon to see NPCs with NPC class levels beyond this range.
Exceptional (6th–10th level): A significant number of national leaders and movers and shakers are of this level, along with heroes and other notables.
Powerful (11th–15th): These NPCs are quite rare; normally only a handful of such powerful characters exist in most nations, and they should be leaders or specially trained troops most often designed to serve as allies or enemies for use in high-level adventures.
Legendary (16th–20th): These are EXCEPTIONALLY rare, and when they appear they should only do so as part of a specific campaign; they all should be supported with significant histories and flavor.
Talk about percentages of the whole population never comes up in this section at al.
Once PCs get up above 13th level, they kind of ARE supposed to be the only ones who cans top the great evil. We want Golarion to be a world where the PCs are the heroes or the legends or whatever. Which means that most of the established groups of high level NPCs you'll see us create will be rivals or outright enemies, with high level good guys generally being loners or rulers of regions.
I'd be fine with saying 1 in 10 NPCs who have stat blocks that anyone would want to bother creating had some sort of spell-casting ability.
But the VAST majority of the humanoids in civilized areas should be commoners, aristocrats, warriors, or experts. Although there's a lot of magic in Golarion... I actually wouldn't call it "high magic." Folks still use lanterns and torches, not magic, to light most homes and city streets, after all.
You can look up various Golarion heads of state's class/levels on the Pathfinder Wiki.