When the cache is created over CLI and even data put in it (also over CLI), that cache is not visible in JON in corresponding cache-container. Also the number of entries (in statistics) doesn't show the entries in that cache.

UPDATE:

Seems that the cache-container in JON shows only 3 predefined caches - default, memcached and namedCache (for local container). In case of clustered container it shows default, memcached and repl. No matter if the other cache is created in the xml configuration itself or over CLI, the cache is not visible in JON UI after server restart.
Also I have tried the other scenario: I have just removed the namedCache completely from the cache container to see what will happen, and interestingly the namedCache is still remains in the JON UI but with red icon which means "Not Available".