I expected "Jag undrar vem är hon" taking "Jag undrar" as one clause and "vem hon är" as a second one... to follow the V2 rule. Is it ok to disarrange the sentence in that way?... For instance as if I wanted to add a preposition... Anyway, I am aware that the way the sentence is presented here is the correct form of it. Then, Should I say this applies for every sentence on that particular form.
The reason the verb isn't in second place in the second part of the sentence is that it's a subclause (this is an indirect question), and the V2 rule only applies in main clauses. Read more about this and about Swedish word order in general here: https://www.duolingo.com/comment/8970470
It's possible to break up the sentence into two main clauses like this: Jag undrar: Vem är hon? ('I wonder: Who is she?') and then you'll get the verb in second place in both main clauses. That won't be an accepted answer here since it's a different sentence. In the spoken language, the line between a quote and an indirect question often gets blurred so that it's hard to tell what is what, but the 'correct' way of saying it is as it's written here.