Knowing that VIC was a "spy cipher" it is unlikely that the agents used a cryptographic device to genreate the 5 digit number but how did they do it?
In the VIC cipher, that significant five-digit number was created by the user when doing the encryption. It was surely made on the spur of the moment without equipment. As you remarked, these people were spies, and they would not have wanted to get caught with some strange device.
The CIA's online library does not mention the five-digit number as a value that the user had to memorize. The agent already had four mnemonic keys stored in his or her mind:
1. a date (in Russian this would be day/month/year; six digits) 2. a snippet of a popular Russian song (20 characters long) 3. the user's personal identification number 4. a Russian word (e.g., the word for "snowfall")
I do not know for sure, but I think it is most likely that agents came up with their own "random" number out of their own heads. One, admittedly thin, piece of evidence might be that the Russians were generating "one-time pads" at that time out of their own heads by pecking at a typewriter--and keys generated in such manner were considered "random" enough to encrypt important traffic.