I downloaded a blank theme and it has a category.php file that's not referenced anywhere in the code, but still appears when I try to view a single category. It also has a main loop that somehow always shows the correct posts without anything being declared anywhere. Is this just a wordpress thing? Is yes, is there some list of all files that will just work when placed in a theme, so I can delete the the ones exclusive to the not-so-blank theme?
Have a look at the following documentation, this should clear things up for you. Your list of files that make up a theme are explained here also. Including which files are used when.