what are the css files with question marks - like modules/system/system.theme.css?pywps6u?
I assume this is resulting from the caching


You are correct. It is for caching; especially to prevent browsers from thinking they have already downloaded a certain file.

If the file was named system.theme.css, and your browser already downloaded that file several days ago, it won't download it again. This results in an outdated site. The suffix changes every time the CSS files change and forces your browser to download the file again.

You can safely edit the 'regular' CSS files on the filesystem. Take care though that is discouraged to edit system and module files, as they will be overridden during updates. Instead create a custom module or theme to implement the changes you need.