mcavic - 4:45 pm on Mar 31, 2010 (gmt 0)
The .htaccess is a good point. But once the server's disk cache has been primed, and assuming the server has enough memory, I can't believe there's any difference on the server side. Especially in Linux, which is particularly good at quick filesystem access and parsing text files.
I wonder if there's a difference on the client side? Does it handle absolute and relative links differently? Do some links take longer to process in the browser cache?
Regardless, as long as your site feels fast, I would definitely go for easier organization and maintenance rather than raw speed.