Your rep has the power to waive these shipping fees and will do so if you ask nicely. They value the relationship more than a few dollars here or there.
As far as I know, Nobel doesn't sell 3Shape scanners. They have their own scanner called the 2G, made by Optimet, which is getting long in the tooth and they just launched a new scanner called the LS3 which is sold under the KaVo brand (sister company) and is feature competitive with the D2000. Their software is now called DTX studio and is a customized Exocad.
If you have Nobel doctors, the scanner is actually very competitively priced, comes with basically Exocad with a minimal licence fee (around $1,000 / year). Not too bad.