It's not that smart
. NXBoot does not (and will never) include any payloads, it'll just be outdated too quickly. The --hekate option just enables controlling Hekate but it does not provide a Hekate payload by itself.
You can place Hekate anywhere and must specify the path to it (just like with any other payload) when calling nxboot. In my examples, it's just expected under its original name in your working directory. You cannot just place it into /usr/bin unless that is also your working directory or you change the path provided to nxboot.
I'd recommend the GUI version if this does not work for you. Unfortunately it does not run on the iPhone 4 (iOS 7).