I read that as showing how he actually cared about _why? as a person, rather than as his persona. He doesn't really care about _why?'s code, he cares that everything is okay with him.
But _why's name isn't Jonathan, Zed didn't know him in person, and in the one public conversation they had _why and Zed weren't on the same side of the argument.
We have no proof that _why is in any trouble at all, and this isn't the first time he's nuked things he created. There's nothing much about the person to be worried about, and the persona isn't real. Zed just likes ranting. (BTW, if you're worried about a person and how they're doing, you don't call them names.)