This isn't strictly an "answer", but I thought you would be interested to see this pot-pourri of spellings of cipher/cypher from the 16th century onwards. It is from sense 5 of the word cipher/cypher in the Oxford English Dictionary. Of course the word began life from the French cuffre (modern French chiffre) with an entirely different meaning (the figure, nought) in the 14th century.
5a. A secret or disguised manner of writing, whether by characters
arbitrarily invented (app. 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.
1528 S. Gardiner in N. Pocock Rec. Reformation I. No. 48. 92 We
think not convenient to write them, but only in cipher.
1587 A. Fleming et al. Holinshed's Chron. (new ed.) III. Contin.
1371/1 Letters betweene them were alwaies written in cipher.
1605 Bacon Of Aduancem. Learning ii. sig. Qq, The kindes of
Cyphars..are many, according to the Nature or Rule of the infoulding:
Wheele-Cyphars, Kay-Cyphars, Dovbles, &c.
1652 J. Evelyn Mem. (1857) I. 289, I had also addresses and
cyphers, to correspond with his Majesty and Ministers abroad.
1749 D. Hartley Observ. Man i. i. 15 We admit the Key of a Cypher
to be a true one, when it explains the Cypher completely.
1812 Duke of Wellington Dispatches (1838) IX. 235 We have
deciphered the letter you sent and it goes back to you with the key of
1837 A. Alison Hist. Europe VI. xlix. 508 Intercepting of some of
the correspondence in cipher.
1885 Gordon in Standard 24 Feb. Cypher letter..which I cannot
decypher, for Colonel Stewart took the cypher with him.