The difference was shutdown would just turn windows off but the machine was still actually running, you could then shut it off once you were sure the disks had spun down or some such. There was something important about raid arrays over scsi on servers that made this important.
The other one just shut the machine down as long as you were using a machine with an atx power supply (rather than AT).
Damn that has been that 15 years or so the last time I saw those options?! Its a little bit fuzzy..