Welcome aboard, BlindWolf. Regarding changing the includes, I had done that in core a while back. However, if you turn on caching, Drupal chokes because of the differences in core inclusions for cached pages. The file that has the function drupal_get_path() doesn't get loaded before the module files are loaded, so it breaks any page request. I'm open to any alternatives, but right now I have to keep them as is in core. Perhaps the answer in the future is to just get rid of the .inc files, but they make keeping track of the code so much easier.

Regarding your second question, I'd always recommend the latest release. People have been using Ubercart on live sites since the early alphas, but it definitely behooves you to stay up to date since so much has been changing. The pace has slowed a bit, but now most of the new release material is bug fixes which you'll want on your site anyways.