The messages can be further encoded with NUCO or OPCODE which can change several times a day.
It's possible that secure digital comms have rendered all this obsolete, but not necessarily so. I'd bet semaphore, light, and flag signaling are still used with both morse code and tactical signal messages.
It's just comms. Sender and receiver agree on medium(s) and protocol(s). One could transmit on ham, the return message could go by light, sonar pings, or pony express. Whatever they agree to use.
Book code is nearly unbreakable if only two or a few operators possess the book. It was used widely in WWII via short wave transmission. A message would likely start with a page number, then a line and choose the number of occurrence of the desired letter and so forth. A bit awkward but quite secure until one member of your comm cell got caught and didn't destroy the book in their possession.
Voice transmissions using something like a Maritime Tactical Signal Book are very efficient and effective.
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Pub. 102 (https://msi.nga.mil/api/publications/download?key=16694273/SFH00000/Pub102bk.pdf&type=view) was always fun to play with - especially with signal flags...
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