Q:
It appears Link information is stored as an absolute path, is there any way to store it as a relative path?
A:
In storing hot links and attachment information, Diagram!2 does store the relative path. In the Link Inspector, Diagram! does display the absolute path name after "Source:" for the user's benefit, but it is actually storing the relative path.
Try this: Create a new folder with a new Diagram! file and a text file in it. Drag the text file in from the Workspace onto an object in the Diagram! file so that it becomes an attachment. Now close both of the files. Go and move the entire folder somewhere else. If you open the Diagram! file you will see that it still has the attachment information. This extends to hot links as well.