The answer is YES: C will by installed twice.
The first installation is under the node_modules folder.
The second in npm v2 manner under a node_modules folder in the directory of the module depending on it.
It's the installation order. Let assume A depents on Cv1 and B on Cv2. If you run npm i A B Cv2 will be nested. If you run npm i B A Cv1 will be nested. The following both chapters of the above link will also cover this theme.