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I always (well try) to comment my code. I have configured my server to remove those comments/extra white space before delivery. Would it be better not to have comments in the live systems code (Javascript/php) and therefore reduce this overhead or remove or interpretation?
If so how can I have my cake and eat it too?
For PHP, it makes no difference. Your PHP code isn’t sent out to the browser.
For JavaScript, it is recommended that you minify your code. This reduces its size by changing variable names, removing white space, and removing all comments as well. There are several online tools for doing this, and it is often available in your IDE.
Whatever you do, leave your code commented where you work on it. Don’t remove comments from PHP, and don’t minify your JS by hand.