Yeah I think you are right. I checked the forums help pages and found this
"It means that at some point you or other users of your computer have installed/downloaded and launched a higher version of NWjs than RPG maker MV uses. It's a completely irrelevant message though and nothing bad happens, since for important settings there is a package.json file inside the folder.
I see this message all the time ever since I downloaded NWjs v.0.30, but no actual errors occur."