Encryption algorithms *might* be subject to attack or decryption... So why not go back to something immune to that: one time pads filled with random noise. These could be distributed to fleet units by courier prior to embarking, or via helo if a unit joined up. A single DVD could contain gigabytes of random numbers for the simple transposition cypher. There’s no algorithm or equation to be broken. No frequency analysis is possible.
“Encryption algorithms *might* be subject to attack or decryption”
The rarest of compromise.
More likely is a traitor from the inside.