Keyboard shortcut for closing the color picker & other tool windows? Command + W won't work
Often for these kind of 'popup'/'helper' windows, the keyboard setup to hide them is the same than to show them.

I tested it in xcode for which the shortcut is :
ctrl+shift+cmd+C
It's comportement is as i expected it, it work as a toggle 'on/off' window/shortcut.

EDIT: Forgot to add one thing, you can find that shortcut easily through the help menu of each app, i usually find myself taping 'show color' to actually see the shortcut and open the panel