Some comments from about a decade ago.
The way it used to work in the Army (that I was in) within a battalion, is that there was a little code book, with a sheet for a 6 hour stretch. Each sheet has a simple matrix for encoding letters, etc. Everyone had the same sheet, and they were created centrally and distributed from there. If any sheets were lost, it was a major disaster.
All soldiers were taught to code up the messages, it was one of the more boring lessons. In practice, corporals and seargeants did most of the coding, but it was still a slow and cumbersome process.
The Army actually has a training course (from 1990) on-line that describes such a system in detail. The cipher system, called DRYAD is covered in https://hosta.atsc.eustis.army.mil/cgi-bin/atdl.dll/accp/is1100/ch4.htm ---------------------------------------------------------------------
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