It seems odd to me that CX would have significant numbers of those cute little rocks going missing.
But then I started wondering, what is the actual rate? If they were referring to only 3 months, that would work out to about 80 per day; and even an airline the size of CX has a few hundred flights per day, giving a loss rate of somewhere in the neighborhood of 1 per every 3 or 4 flights (depending on just how many use the rocks). And if the few months referred to a longer period the numbers only get lower. Then run it against the number of J/F pax serviced.
IMHO this sounds like a breakage rate with some additional losses from items walking out the door with pax. Especially for the tea sets, which I have seen broken by FAs (if they drop, they are history).