I remember reading in Bruce Schneier's Applied Cryptography that in some cultures "encrypt" refers to the process of entombing bodies for burial and that "encipher" did not have that baggage.

Similar connotation to "decrypt" which would be exhumation.

For example in Spanish, there's been always a fight between using "cifrar" instead of "encriptar". I like "cifrar" a bit more, but it's true that we've always had the prefix "cripto-" for hidden or mysterious things. Anyway, the difference is "cifra" is the Latin root for "digit", and "kryptos" is the Greek root for "hidden".

What comes to my mind is that decipher has a well established common meaning, but decrypt just means "dis-encrypt".

I've no idea why it died out, but it certainly seems to have.