My solution might not work for everyone, but it solved my issues today, I had nw.exe refusing to unload if and only if I launcher the game from inside Steam, if I launched from the steamapps/common folder I had no issues and retained all steam integration... For me it had everything to do with appData/Local/TEMP decompression of package.nw and steam file logs and I am kind of happy I had this issue because for me I can see the benefits of not decompressing package.nw each time I launch the game, instead loading from the install directory. I could waffle on about it all but in the end these 4 simple steps fixed my problem and I now have everything back to normal , zero bugs and no ghost instances of nw.exe in my task manager, steam agrees with me when I window.close.
If someone would like to try the same process and share the result that'd be great! I have a feeling though it's not a one-size-fits all kinda' deal.
Basically, we're loading package contents directly from install folder instead of decompressing them to a TEMP folder.
1. rename package.nw to package.zip
2. extract to package/
3. inside package folder cut package.json out and paste in root folder next to nw.exe
4. open package.json and change at the top "index.html" to "package/index.html"