I thought the only meaning of cipher was "code." Apparently not. From a Slate article about McCain's and Obama's invocations of Henry Kissinger's thoughts on negotiating with other countries:
Apparently, (Kissinger) does not know that the envoys of the Iranian foreign ministry are only ciphers, easily overridden by the mullah-dominated "Guardian Council" that holds all real power in Tehran.
The first meaning of cipher is "zero," according to both Merriam-Webster and the OED. Thus, by figurative extension, it can mean what the Slate author used it to mean, "a person who fills a place, but is of no importance or worth, a nonentity, a mere nothing," as the OED puts it in definition 2a.
Cipher as a code is all the way down in the fifth definition in the OED:
5a. A secret or disguised manner of writing, whether by characters arbitrarily invented (apparently the earlier method), or by an arbitrary use of letters or characters in other than their ordinary sense, by making single words stand for sentences or phrases, or by other conventional methods intelligible only to those possessing the key; a cryptograph. Also anything written in cipher, and the key to such a system.
According to the OED, cipher comes from the Medieval Latin cifra, which comes from the Arabic cifr, which is the name in Arabic for the arithmetical symbol for ‘zero’ or ‘nought.’ From that, cifr came to be used to mean "empty, void." The OED also says cifr was a translation of the Sanskrit sunya, which means "empty."