To regard these letters as ciphers is a precarious hypothesis, for the simple reason that cryptography is not to be looked for in the very infancy of Arabic writing.
Cryptography had a great fascination for Wheatstone; he studied it deeply at one time, and deciphered many of the MSS.
This non-Semitic system, which is found, in many instances, on alternate lines with a regular Semitic translation, in other cases in opposite columns to a Semitic rendering, and again without any Semitic equivalent at all, has been held by one school, founded and still vigorously defended by the distinguished French Assyriologist, Joseph Halevy, to be nothing more than a priestly system of cryptography based, of course, on the then current Semitic speech.
Facts of this character taken by themselves would perhaps be sufficient to convince most philologists that in Sumerian we have an arbitrarily compounded cryptography just as Halevy believes, but these facts cannot be taken by themselves, as the evidences of the purely linguistic basis of Sumerian are stronger than these apparent proofs of its artificial character.
Certainly no cryptography based exclusively on Semitic could exhibit this sort of interchange.