They are selling products and there is no order data--the store part has never been live. Cleaning out both ecommerce modules is potentially feasible. There is a "guide" to this on the Ubercart site, but the lead there (who wrote it) recommends against it. :)
In terms of the overall upgrade to 6 - is this a stock theme and are there upgrade paths to 6 for the modules in use. Sites that are done wrong in 5 can be a problem to move to 6. I have ran into that trying to move my first attempt at Drupal from 5 to 6.
Yes, I had the same thought. The theme is custom and the site has a bunch of modules--not all of which I think are even used.
Fred, I know you know this but I will say backup everything before trying this.
Several copies of the site already exist. :)
Thanks!