Usually words with a distinct Latin etymology take in- as a negative prefix, and others take un-. Now one could argue that the origin of decipher is the French déchiffrer rather than its lain root cifra... but I would perfer indecipherable.

I would normally use indecipherable.

As a general rule, one can add the prefix un- and the suffix -able to a verb if the meaning of the verb is unchanged; so if a careful writer wrote undecipherable, I might surmise that they wanted to indicate that they did not intend the normal meaning (difficult to read) but the literal meaning (impossible to decode - without access to the appropriate key, presumably).