In the case of Erlang, for instance, it provides a built-in remote shell which allows one to connect to a running Erlang process, get multitude of information about the VM, loaded code, etc.
As long as there is a convenient way to maintain a running system, that same way can be used for hacking.
My point is that the whole workflow of creating and deploying applications becomes much simpler as the final VM can be an (almost) disposable item, rebuilt at-will. This is pretty much what the configuration management tools are all striving for but Unikernels work this way by design. Therefore, our notions of managing such systems will also change.
[1] http://amirchaudhry.com/from-jekyll-to-unikernel-in-fifty-li...
I've been doing Project Euler in OCaml recently so this is a perfect excuse to expand my horizons.
[1] http://www.somerandomidiot.com/blog/categories/mirage/
[2] http://openmirage.org/blog/welcome-to-our-summer-hackers