Not really, both rely on nodejs+chrome. Main difference is the approach on mixing those two. In nw, starting point is a .html file ; in atom-shell you start with a .js file and create a window from there. Atom-shell is backed up by github, so it won't go away any time soon. Fun thing is that top contributor (zcbenz) to atom-shell is also the second top contributor to nw. Almost as if he created his own, better version of nw with hook... khm... easier build process and context management. Anyhow, for now i'm with node-webkit, i just threw this outhere because i think it would be wise to watch how things develop further down the road.
Also; not sure in what do you mean with more low-level interactions. Node can do low-level quite good... Can you expand on this?