Web Scripts are (in general) the best way to programmatically access all content in Alfresco from some other system, no matter where it's stored (DM or WCM).
As for selecting whether DM or WCM is the most appropriate repository for a given use case, it's better to try to answer those questions I asked earlier and decide based on those capabilities. Both repositories have equally good support for the physical storage of files (regardless of what types those files are), the differences are more in the additional services that Alfresco provides above the raw "filesystem" layer. At some point the two repositories will be harmonised and the differences won't be apparent, but for now DM is stronger on the transformation / metadata extraction side, and WCM is stronger on the sandboxed content production, versioning, workflow and deployment front.
Cheers,
Peter