Kevin Schroeder has posted the results of some research he did around using the "AllowOverride" setting in Apache. He found some interesting differences when it was set to "all".

Commonly known as .htaccess, AllowOverride is a neat little feature that allows you to tweak the server's behavior without modifying the configuration file or restarting the server. [...] Beyond the obvious security problems of allowing configuration modifications in a public document root there is also a performance impact. What happens with AllowOverride is that Apache will do an open() call on each parent directory from the requested file onward.

He includes the output from a strace call in the post - first showing the function calls with it set to "none" then the same request with the setting on "all". More "open" calls are being made in the second run, increasing the execution time by a decent amount.