Mmh, there are many names that are commonly thought of to be something that they aren't and where an older association has been lost (f.ex. today nobody, including myself, really knows that "Jenny" was originally derived from "Jane"). Even more in Japan where imported names are rare and usually there is no need to search for the origin of a name in a different language or country.
So today Naomi is a really normal japanese female name, but concerning the origin apparently at that time it wasn't. Else the author wouldn't have chosen that name and described it as "Western", like you said :)
In fact, the article doesn't say that Naomi started the fashion of names ending in "-mi", but quite on the contrary. At that time names ending in "-ko" where still popular and Naomi was too new, too modern, so it didn't became used widely until after WWII. Maybe because like you said other names with "-mi" were used as well, so it didn't sound too foreign anymore. So if that is true, I suppose it is quite normal that the name has lost his western image over the years.
The fact that Naomi was/is also used as a male name, doesn't seem to be a well known among Japanese people either, maybe Tanizaki Junichiro didn't know about it either ;) (By the way, I also can't find any male Naomis before 1940 more or less, do you know any others?)
I know that content from wikipedia should always be verified twice, but I don't think it can be completely wrong either (any idea for some other sources maybe?). So for the moment I still feel like it's a piece of information that should be added to the entry.