Yeah your totally right. I just completed my first work unit and the next one is totally different.
Now I'm working on p2420 Ribo alanine aux. There are only 250 frames at 6m:48s/frame! +/- 1day 4hours to complete.
This protein is friggin huge in comparison too. ;p
If they're using the same client I still think the average times people are posting are decent indicators to their system speed. People with e6600's for example posted around a day per work unit. More or less depending on whether they had over clocked or not.
Your assumption of more or less a day per WU for SMP is pretty good for a C2D, especially if you are new to folding. After a while you will get a feel for which ones are faster, which ones are slower, and how long they should take on your particular setup.