Actually, the files that have a class name in their name are the ones already documented on the Python API page.
The additional functions that you can directly call in Python are defined in CyGameCoreUtilsInterface.cpp and implemented in CyGameCoreUtils.cpp/.h and are not part of any object like CyGame or CyPlot. Their definitions do not have the python::class_<CyThingy>("CyThingy") item in them, which would probably be why the script that built the API page didn't find them. These functions are, I expect, included via the ubiquitous "from CvPythonExtensions import *". They are all wrappers for similarly free-standing )not part of a class) functions in the DLL (most, if not all, of which are actually implemented in various .h files, rather than .cpp files).
This is where you'll find isWorldWonderClass, isTeamWonderClass, isNationalWonderClass, isLimitedWonderClass and a bunch of others.