Avoiding Spotlight to spin up external drive
Yes, this is pretty annoying behavior, especially if you have multiple hard drives connected to your Mac, and to my knowledge there is no way to prevent Spotlight from doing it.

Fortunately, most app launchers such as LaunchBar, Alfred, Butler, Quicksilver, etc. maintain cached file databases, so they don't spin up all your drives whenever you use them to launch an app or to search for a file. They also have a ton of other useful features. I personally would recommend Alfred or LaunchBar.