You can read Brad Setser's own thoughts on this here, although he doesn't really go into too much detail as to why he believes China would attempt to "hide" their forex reserves.
Indeed, if you read the full article, you'll find that these reserves aren't so much "hidden" as moved from one department of the Chinese government (the State Administration of Foreign Exchange, SAFE) to other departments (the soverign wealth fund, state-owned commercial banks et al.), although Setser does make vague hints at some kind of shenanigans. The reason a government would do this is that, while some forex reserves can be beneficial, it is usually considered undesirable to hold huge reserves of a foreign currency, and circa $3tn is pretty huge, even by Chinese standards. After a point, it is more attractive to convert that currency into foreign assets, which can yield some sort of return. China has chosen to do this via arms of the government other than the SAFE, which isn't unusual per se.
As a separate point, note that governments usually like to keep the composition of their forex reserves secret. Indeed, the IMF claims that only four of their staff have access to this data at the individual country level. However, this is not what is being alluded to in the article that you have quoted.