There's a Launchpad Manager app (or two), but you could always just move the icons into a "last page" of the Launchpad, so they won't bother you.
There are a lot of similarities between the iOS Launchpad and the OS X Launchpad, and one is that the apps in your Applications folder will show up as shortcuts in the Launchpad. You can arrange the shortcuts any way you like, but if you delete them (via the X) I think you're also deleting the app.
So far, that's as much as I've been able to fathom of this.