Is it possible that rather than cheating customers, they are simply trying to increase the density of the paperweight to make it more effective?
It would be pretty funny if there was some kind of scam going on here where the notes were actually being reconstructed and a small portion of each paperweight was siphoned off to support the crime (perhaps by diverting whole notes early in the shredding process). That could explain why some weights had fewer notes with rocks to make up the difference. Seems unlikely obviously in reality but there should probably be an investigation to figure out why the Hong Kong Monetary Authority visitor center is participating in fraudulent behavior.