Documents are a HUGE part of any management system for me so here are some quick thoughts:
I see nothing wrong with having duplication of files - it basically works like a backup system. The challenge is making it streamlined in the work process so one isn't unnecessarily slowed down by having to get the file into the file system AND opengoo.
Folder <-> Opengoo "sync" is one way to accomplish this but I see that as being very challenging and time consuming from a technical standpoint. Rather than sync folders, I would suggest scanning a root folder for all files (via cron or whatever) and automatically importing those files periodically so the user can go through the list and quickly attach them to workspaces. I wouldn't bother preserving the folder structure exactly in opengoo, and let the user worry about how the files get onto the server (mapped drive, local upload cron, whatever).
Another possibility is just a quicker and easier way to get the document into Opengoo via the interface - right now one has to save the file locally, go to opengoo, click new upload, select the file, describe it, click "upload" ... that's a lot of clicks! That is why I suggested a 'drag-and-drop' onto the workspaces as an alternative in another thread. Other web apps use this (see drag-and-drop attachment feature in TiddlyWiki).
I also plan to write a little script for Ubuntu which will let me just right click a file and select "add to Opengoo" which will just directly import the file (to be classified later). Should not be too hard to do. Little scripts like that might help solve the problem, at least for now.
Finally, you might consider a third (or fourth) option for storage: Amazon S3. Note that this has been implemented in the railscollab fork of projectpier:
http://github.com/jamesu/railscollab/tree/master (might be based on a ruby S3 library though; not sure if an analogous one is available for php).
As always, keep up the great work!