GCHQ can't crack WhatsApp encryption.
They wish they could, and the government has just passed a law to try and make that a possibility (but probably not, because encryption backdoors are insanely stupid), but yeah this isn't anything. WhatsApp is stored on-phone for the most part, with only the most recent messages stored on their servers. If you throw a phone away and don't have it backed up then that's it.
However - that doesn't mean, of course, that the people on the other sides of those conversations don't have their phones still, and it should be within the remit of an enquiry like this, in this kind of situation, to say "OK well you were talking with this list of people who are relevant to this, so we're going to subpoena them instead and piece together your chats from their side." And for some people that might already be possible too.