>but then again, why would she call him kon-el?

I think Wonder Girl either recognized his voice or she is just crazy with sorrow and is hoping it's him.

>My guess at this point is that she's wrong, but that's a big
>teaser to put in there. I bet they leave us hanging on it for
>a few weeks.
>
>Has any reference been made to Supernova in any OYL books?

Yes, there was a headline, on the Daily Planet, in the initial Superman OYL arc referencing him.