@Harlequin: No, the Store app talks directly to SkyDrive. I really wish that it would fall back to the local cache if there was no connection, but that's another issue altogether.
The SkyDrive folder in your user directory contains folders from SkyDrive that are sync'd locally. Anything you do in that SkyDrive folder is reflected in the cloud, and any other computers that you have the SkyDrive service installed on them. Rather than deleting that stuff, you can right click on the tray icon, go into settings, and there's a Choose Folders tab. That will allow you to get rid of locally cached content without doing anything drastic.