||Start Me Up: Writing and Understanding OS X StartupItems|
Response to: Stop
Personally, I've found that servers need to be (deliberately) shutdown so rarely that it isn't a hassle to shutdown the relevant processes manually before telling the machine to reboot.
If it goes down for some other reason (lightning, blackouts, people tripping over power cords... none of which should happen to properly set up servers) then the shutdown scripts wouldn't be called anyway.
It's a convenience thing, but it's not really a necessity when it's used fair less frequently than many other useful features of Mac OS X.