Welcome Cleaver.
The themes are critical by nature.
The author is working within genre conventions and is examining the tropes and how they apply to who we are as readers.
The most important and common theme in fantasy is the triumph of good over evil. This, and the idea of pre-determined fate versus self actualization are the primary themes in PoN.
We are not given easy definitions of good.
There are few characters who provide easy analogues for ourselves that we can dub as being 'good', and the question of evil is also muddied.
Earwan social systems preach a kind of Aristotalean ideal of 'good', embodied by Proyas. Esmenet and Xinemus present a Stoic philosophy. Akka embodies socratic self criticism.
Kellhus is clearly the Nietschean extreme of the self actualizing ubermensch, but because his objectives are bent towards missions of domination it is difficult to see his amoral methods as 'good'.
The carnal selfishness of the consult provides a straightforward and obvious antagonist, but by introducing variations on the romantic philosophical notions of LeVayan satanism - some readers feel that they may have a point in the face of some of the absolute impositions that the social restrictions of three seas culture and religion presents.
So, rather than implying that any philosophical system is 'the best way', the author holds up these philosophical problems for the reader to consider.
I heartily recommend spending a little time on Wikipedia having a look at some of these concepts if PoN has whetted your interest.
I'd suggest browsing Platonic ideals, socratic method, Stoicism, Aristotlean ethics, moral ontology and epistimology, and self-actualization as a way to gain a better understanding of the basic philosophical themes.,