Hi,
Personally I delete all cookies every day. It's just another way of tracking your movements, there are some sites (banking etc) that need cookies enabled to function correctly but I do not find my connection to any site slowed down due to my cookie deletion.
Remember that they are also being cached in memory and written back to the Cookies.plist file periodically. So if your happy to use terminal possibly the easiest way to do the above is to create an Automator action or Terminal.app script that does it for you and then just run the action/script manually once a day or so. But I like to do things manually so I know what is happening and have control.