I know that but will the scenery work on seperate hard-drives?
Yes, it will work without a problem. Just not automatically. If you had FSX and FS9 under the same Windows installation, activating one version will automatically have the other one active as well.
Instead, under 2 separate Windows installations, you need to activate them separately on each OS, by using the "Register Serial" function of the Addon Manager to activate your Serial Number on each OS.