The only problem is passing values to the exe or getting values back. You could use the clipboard for this but that's a bit hacky. Another option is using a file to return the data, but it's not ideal.
Outside of that there appears to be plugin for nw.js to communicate with other dlls or you could make a plugin. The problem is, to do either you need to re-compile the nw executable, and unless you're very familiar with the process, it won't be easy.
Would it be possible to make the program with js instead? That is if you made it. That way it's very doable to make a c2 addon that communicates with it.