In FF3 if you include the code as a module then FF3 will try to parse it and show its functions in the Explorer. FF3 will also move certain things from a module to the CODEGEN*_DECLARES.INC file such as TYPEs, MACROS, GLOBALS, etc.... Files in a project via #INCLUDE's have nothing done to them. They are simply compiled into the project.
FF3 does not do anything special related to determining if a function is called or not in a project. It includes all code in the final EXE unless, of course, if it is specifically excluded via conditional compiling (%IF %DEF, etc...).
I guess that in theory compiles would be a fraction faster if the code is #INCLUDE'd rather than put in a MODULE but I bet it is not noticeable unless the MODULE is very, very big.