I know that the geometry for the Vamoots/Compact changed from 2005 - 2006. I had a 2005 Compact SL (which had the same geo as the standard Vamoots/Compact) and the headtube was shorter than the 2006 version. Don't know if that geo went all the way back to 1998, though.
My guess is that, aside from the obvious differences (i.e., the 1" headtube and the geometry), Moots has made other subtle changes over the years (source of tubing, etc.). I'm sure that a '98 Vamoots still rides beautifully, and with updated components would hold its own against bikes made today. Again, my guess is that the 2010 is going to be a bit more responsive and laterally stiffer, which you would notice when you really pushed it in turns, etc. I'm sure the '98 would be a great buy regardless.
If I got Moots of that vintage, one thing I would do is replace the fork. I believe that there are some NOS Ouzo Pros still around, and Serotta is now making the S3 and F3 with 1" steerers.