I think there have been more changes in those 18 years than many would think.
Looking at averages from back then to now, ball in play time has increased by almost 10%, the number of rucks by over 20% and the number of tackles almost 35%. So, a 9 would have more breakdowns to get to and be covering more ground than they were c.2004. Also the number of box kicks and therefore kicks a 9 is making have increased - back in 2003 for example only 6% of kicks were box kicks, now around 25% of kicks are and that will increase the workload on the 9.
You could equally ask why we change props when in 2003 the whole Woodman, Thomspon and Baxter played 100 mins and Vickery and Young were only changed in injury time.
I had a look back and the change started to happen around 2010-12, for example in the 2011-12 season we had Nic Berry and Joe Simpson regularly swapping at around the 55 min mark.
I do think any professional scrum half could play 80 mins and still have some running in them but I also think that it is one of the positions where a change can re-energise the attack.