1). The programs simply "refer" to the elements contained inside of them. That's the beauty of the structure: Mutlisamples in one place, and .sfz files define their properties. Elements add another layer of functions, and Programs group those together with more functions. No duplication: it's just one streamlined pyramid of building blocks with "maps" at each level.
Just to clarify, though: When you do your drag 'n' drop reorganization, either left-click and drag, or right-click and drag with the Move To option. Copy To (the destination) will create a duplicate.
2). Save As ... will duplicate the Programs themselves. If they contain outside Elements that are already saved somewhere else in isolation, it doesn't duplicate those in a sense. But it does group all of the variables together for all 4 Elements and save those, along with some other parameters. Save alone will overwrite the original program.
Concerning file size, though, .elem and .prog files are very, very small. It's the Multisamples that carry the hefty weight, and those don't get wrapped up in the files (only 'pointed" to). That's why if you start moving the Multisamples around, the Programs may not find them. You have to "redirect" Dimension Pro to where they're at, and Save the Program again.
3). Bonus Answer: I saw your question a few days back about Modulators in the Sonar forum. Check out the
Dimension Pro section at the
Project5 Wiki for expanded information.