“Which” is referring to "various ways" as a relative pronoun. In this case the priority is given to the noun closest to it. If you say “one of them” people may think you are speaking about “e-books and e-readers”. The increasing popularity of e-books and e-readers is affecting the publishing industry in various ways. (not ,) One of them is the rapid decline in the sales of printed books. See yourself as it is neither so clear nor so clean.

My question is why put which and why not just use one of them? = The use of "which" here is okay just like you can also say use of "them". "which" is used here to give emphasis on the particular reason compared to if you use "them" it is saying that it is just one of the reasons why but it is not most important. If you make use of "which" just like in this context it is saying that it is the most important among all the other elements.

I see no mention of relative importance. A gree with ppereira's answer, but would add that using "which" is also simply neater and shorter.

yes, it's a good question. I wanna also know why use here "which", why not "them"?