Nanobox provides actions you can run on servers such as restart, reboot, rebuild, etc. In rare cases, you may have to login to your VPS, but provider integrations simply tie into your hosts api, so you should be able to completely manage the server from nanobox.
If you're running a server cluster, Nanobox monitors the cluster and will remove a node from the routing rotation if it goes offline. It will automatically try to get the server going again. Once it's responsive, it'll drop back into the routing rotation.