Almost every APEX Developer knows that JavaScript and CSS belongs in separate files and (in 99% of the use cases) not somewhere in your Page properties. If you have this code in separate files it is easier to use them in a Version Control System (SVN or Git) - if the files are outside of APEX. And the code you store in these files can be reused, in contrast to the stuff you store on Page level. In a lot of environments it is harder to use external files, because deployment of these files to the appropriate location on a webserver requires special privileges that not everybody has. In those cases storing these files as Static Application Files or Static Workspace Files might be a better solution. It makes deployment easier, because these files will be exported and imported as part of the application. You can't accidentally forget about them. But working with these files is quite a pain. When you need to edit something you have to download that file, make the changes, upload it again...