Homebrew and usr/local/include/ question
I would say yes. Homebrew will re-load any files it needs next time you install or update or have an error compiling a package.
To be safe, make a backup of the Mac - Time Machine is fine for this. Things in /usr/local aren't from OS X so you won't cause system issues removing these files.
brew rm node
The above command should clean up node.js and you could re-install it after cleaning up if you need it.