Certainly if both computers have the exact same username and path for each shortcut, then what you mention is simple. If not, then I'm stumped as to how you'd synch shortcuts (that have specific paths associated with them) synced accross 2 computers where the paths don't match.
But if you do have exact same User name, life should be good with drobbox (etc.). Add your desktop as one of the sync folders. Initially it will be messy if you already have shortcuts on your desktop. You may want to wipe one of your desktops clean (empty), then start the sync from the computer that has shortucts on the desktop. Though I have never sync'd the desktop folder, I would hope it's like any other folder.
The next issue would be making sure each new shortcut was added to the same fence. If you use Portal, then it's a non-issue. But if you are using ad-hoc fences, there will be some manual intervention. This is where the developer may be able to help and possibly the above Registry step may come in handly. But I have not looked into the above suggestion at all. "AppData" suggestion looks promising after initial glance though.
