To one as young as you, I’m sure it seems incredible, but to Nicolas and Perenelle, it really is like going to bed after a very, very long day. After all, to the well-organized mind, death is but the next great adventure. You know, the Stone was really not such a wonderful thing. As much money and life as you could want! The two things most human beings would choose above all – the trouble is, humans do have a knack of choosing precisely those things that are worst for them.
I guess the second it indicates to die or death, and the first it indicates “Nicolas and Perenelle ~ adventure.” I guess “those things” has no its match in the text, but it implies the worst concrete choices one makes in his life. Are these right?
It seems to me OP’s first “it”, like my first one here, is simply the dummy/existential “it” of “It’s raining.”
Possibly the second one stands for “death”, as mentioned in the next sentence. But strictly speaking it refers to whatever was being described in preceding text we haven’t got here (which may very well have been writing about “death” anyway, but that’s somewhat beside the point).
Including the word those is an entirely optional stylistic choice. It refers only and exactly to “things that are worst for them”. It could be omitted, or replaced by, say, the very things…, without changing the meaning in any real sense.