For example, the window that lets me view my keyboard layout does not have a launcher icon. The Unity launcher show a grey question mark instead, which does not feel pretty. Having more than one such window open is not only visually displeasing, but cumbersome to navigate. When finding these cases, should I file a bug? Or do design quirks not belong on Launchpad?
Yes, application windows that do not have appropriate icons, WM_CLASS, and other metadata set, should be considered a bug in the application that provides those windows.