Back in the late 90's and some of the very early 00's, it was actually pretty common to not just know girls on the internet but be friends with a fairly large age-range of them. I won't go into detail about how or why heavy gender segregation happened, mostly because I don't fully understand myself and it's not on-topic to offer my speculation anyway. But I will say that the idea of heavy gender segregation in culture at large is a relatively brand new thing on the scale of the last four decades or so.
Relatedly to the chapter though -- I think it is in fact unusual for boys and girls in Japan to be casual friends. Unless they already knew each other from childhood, they're coworkers at a job, or if they're members of the same club. Yoko was probably perceived as really dysfunctional by her community. Which to be fair, is pretty in-line with her characterization thus far.