Answer point by point.
1. First, these resources need not the OS and the programs that use them (except for the manifest). But the OS (or rather, the win32api library) provides a way those same resources to obtain. The DLL any functions responsible for issuing resources, no (but there is a subtlety — some old programs to get online, downloaded the library as an executable and thus caused its initialization — this used some viruses). In addition, the format of the executable and its resources conventionally-known, and can work with the resources directly, bypassing the special functions. In this way, by the way, is ResHacker.
2. Example of creation, I do not know. But if you know at least one Resource-only library, you can delete all the resources and get "clean", which you can then put any other resources. Method completely correct, and, most importantly, eliminates the need to get acquainted with the compilers and compiled programming languages.
3. The Desktop File.ini is a declarative configuration file, not a mandatory program, so, strictly speaking, in this line, nothing happens. Instead, this line tells any application that can understand the file Desktop.ini that for file display
3D Vision Photo Viewer.lnk
you should use the line number 2003 for the current locale resources from PE file
%ProgramFiles(x86)%\NVIDIA Corporation\3D Vision\nvstlink.exe
About the format of the Desktop file.ini well written in Wikipedia