Where does the dosbox version of SC2K actually save cities on my harddrive (I'm running Windows 7 64-bit). Within the game GUI, it indicates that it is saving files under C:\CITIES. But there is no corresponding C:\CITIES directory on my harddrive. I also checked the game installation, directory, C:\Program Files (x86)\GOG.com\SimCity 2000 Special Edition, and did a search on my entire harddrive without turning up anything,

Installing the game in C:\Program Files (x86)\ means your saves will be in (user name)\AppData\Local\VirtualStore\Program Files (x86), I think this folder may be hidden.

Where did you mount "C:\CITIES" in DOSBox?
Try looking at where you mounted it. You had to mount it from somewhere on your actual file system.