Near the end of the game, Cissnei ended a conversation with Zack telling him that "Cissnei" is not her real name. Although she never had a chance to tell Zack (and the audience) what her actual name is, the Crisis Core development staff mentioned in the Keywords Collection from the Crisis Core: Final Fantasy 7 - the Complete Guide in Cruise Story & Visual Archive that the name Tian was another code name they were considering for Cissnei during development.3
It is interesting to note that, similar to other named Turks members who have made apperances in Crisis Core and other titles in the compilation (namely Tseng, Reno, Rude, Elena, and Veld with the exception of Vincent, who is an ex-Turk member), Cissnei was not given a last name. Arguably, Cissnei is a code name so it is resaonble that a last name is not required, but does that also mean that Tseng, Reno, Rude and Elena are all codenames? Perhaps the Turks require its members to use codenames because of the shady nature of the types of work that they are known to handle, from surveillance and reconnaissance to assassination and kidnapping, the Turks work in the shadow. Comparably, SOLDIER, particularlly the 1st class members, tend to use both first and last names (with the exception of Sephiroth). Unlike the Turks, SOLIDER members are the elite fighting force of Shinra with most of them seen as heroes within the company and amongst many citizens of Midgar.
Cissnei's name is written as シスネ (SHISUNE) and is pronounced similarly to how you would say her name is English. As with most of the characters in the compilation, I doubt the development team intended for any of them to actually have Japanese sounding names, but rather the “Japanese name” exists as a pronunciation guide for Japanese players to be able to say those names.
Perhaps Cissnei's name in Japanese came from the word 静か (shizuka), meaning tranquility or calm, which is reflective of some of the characteristics she possesses and, in my opinions, serves as a sensible codename for her.