The changes I described for the Ninja is actually a single feature, that will be added on top of existing content, namely the Ninja class (which is an alternate class of the rogue):
https://www.d20pfsrd.com/classes/alternate-classes/ninja/The problem however, is that the rogue got 3 new features in its update, which is known as the "Unchained Rogue":
https://www.d20pfsrd.com/classes/unchained-classes/Rogue-unchained/#TOC-Debilitating-Injury-Ex- It is largely the same as the original rogue, but also has the Finesse Training, Debilitating Injury, and Rogue's Edge features.
This Unchained version sadly has forgotten about the Ninja, which is slightly better than the rogue with its ki pool, but not nearly as good as the Unchained Ninja. An existing full homebrew exists for the Ninja, but some DM's noted that they found it a tad much. As such, this single feature (Ninja Finesse) is meant to be taken on top of the standard Ninja, which grants it additional options.
I apologize if this may seem a tad complicated, but the ninja has quite a history behind it in Pathfinder, and this is meant as a bridge of sorts to give them some much needed love.
This is also why I made "Unchained" quoted, since Unchained is a term used for a number of updated Pathfinder classes, and unfortunately they did not make one for the Ninja.
As for the Nokizaru, they are based on a ninja clan known for its trickery. This gave them a reputation for being "monkeys" or using magic. A few other content creators have tried to create them, but I felt that their versions were a bit lacking. Mine was a bit more "bland" if you would, by basically copying the Eldritch Scoundrel Archetype for the Rogue. However, this felt fair to me seeing as the ninja is just an altered version of the rogue, plus I made them gain their sneak attack earlier than the Eldritch Scoundrel, seeing as the latter has more trickery and the former is more about killing targets. Hence the references.