It's a way of telling the reading device to load a CSS file based on the screen size or orientation
Here is a good article to explain further into the subject:
http://epubsecrets.com/media-queries-in-epubs.php
Here is an example of a book using media queries:
https://code.google.com/p/epub-sampl....epub&can=2&q=
Why would you want to move those to a separate file? some ebooks readers does not have support for these queries and disregard the entire file because of that, you don't want all your eBook CSS disregarded because of one media query the device doesn't like.