In Hikaru no Go, Waya's username when playing Go online is Zelda. In the anime the reason wasn't explained (I haven't read the manga, so maybe the explanation is in there). The first thing I think of when I see the name Zelda is The Legend of Zelda video game franchise, so I tried to find out if the username was a reference to that, but I couldn't find out anything online. I'm interested in both Waya's reasons (if available) and the author's for using the username Zelda.
There is no explanation given in the manga about Waya using the nickname "Zelda".
However, the adult person explaining computer/internet go to Hikaru says something like "Mmhh, with a nickname like 'Zelda', this person is probably a kid. On the internet you never know..."
This helps Hikaru to understand that Sai can play on the internet without giving away his true identity. Because "Zelda" is a nickname anybody can choose. It doesn't give away anything on your identity. You could be a boy or a girl, a teenager or an adult, ...
I believe the nickname "Zelda" was chosen (by the scenarist) because, like you said, anybody knows about "the legend of Zelda" reference even if you didn't play the videogame. Having a person saying "His nickname is 'Zelda', he must be a kid" is something every reader will understand.
Furthermore, Waya knows how to handle a computer and we can safely assume he plays videogames. Akira and Hikaru are all about go, but Waya is more a "normal" or "typical" teenager. Even if he is an insei, he has other interests than go.