Haven't checked whether a scanner actually finds it there, I just made a craft and while testing it, I extended the drill right in the center of the launchpad and started getting Kethane, followed by the green smoke so it seems normal but I tend to see any surprise as potential disaster waiting to unfold. It's pretty convenient though, cause in the past I'd build something only to send it to the moon to realise I didn't assemble them right, so now I can simply test it on the launchpad.