Technically, there is no need to run npm update for packages other than nodebb-* packages. So all you really need to do is npm install.
However, you'd want to update the nodebb plugins/themes, so:
ls nodebb-* | xargs npm update // I do not take responsibility for this command, if it burns your house down...
If you run into errors specified by #6, please do an npm rebuild to patch that right up.