Why is Waya's 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.