lammert - 9:03 pm on Mar 30, 2010 (gmt 0)
There is one reason I can think of why uploading everything to one directory might give a (small) speed difference. If the files are at the root level, only one .htaccess file is parsed with Apache. If a file is deep in a directory structure, all the .htaccess files are parsed recursively. But 20-30% seems to be a lot to me. There are too much other variables which have to be taken into account to come to such a definite conclusion IMO.