Calligraphy is considered an art form by many, and is typically used not only among shugenja, who use advanced ciphers and scripts to protect their mystical secrets, but also by artisans and courtiers, who use it to impress others as part of their complex schemes to gain favor in court. Training in calligraphy is not necessary as part of literacy, as all samurai are literate, but it does allow one to show refinement and sophistication.
If you possess the Cipher Emphasis, you are assumed to know one cipher commonly used by your Clan. Ciphers can be very difficult to break, with varying TNs depending upon their commonality of use and means of creation. Typically, the TN to break a cipher is the result of the Calligraphy (Cipher) / Intelligence roll used to create it. The High Rokugani Emphasis is used to make use of the ancient, florid, and sophisticated style of language used in the Imperial Court.
Note: The rank 3 and 7 mastery abilites are house rules and are not part of the standard 4th edition ruleset.