Hundreds sometimes even thousands of database changes go in daily by several of us, at a mysql prompt, through the PHP editor, and even in-game. While everything is logged, it would not be feasible for me to round them all up and put them into update files. I'm lazy about the current system as is which I've made largely automatic.
Separating the tables isn't a great idea, because as GeorgeS said many tables inter-connect making it real easy to make a mess of the DB if an update gets fudged.
I like the single file mainly because it is as fool proof as one can get with DB sourcing. You don't have to worry about missed or outdated updates, conflicting data, etc. People manage to mess up the current system as is, I couldn't imagine the support requests I'd get if I separate the files or offer individual content updates.
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