I thought that an explanation could be that the logs are sent to the server asynchronously and if the application gets killed before they are sent you don't see them in the crash report. I checked and that is not the case: even if you wait for a while before calling the default handler nothing happen.
The only explanation for now is that Crashlitycs uncaughtException handler is called before mine.
So to fix the issue it is enough to register the handler after calling Crashlytics.start