I was previously using phonegap CLI (3.0 till 3.3) and www/res/icons were here when creating new project but actually not copied to the platforms when creating platform or building. Actually they were used only for phonegap build.
I'm now using cordova 3.4 and www/res is no more created.
The default icons are created by the cli when you add the platform to the project. You can change the icons after you add the platform, the CLI will not touch them when you build, so you only have to to it once for each platform.