As you said, the video card plays no impact on the web scene generation. However I did notice that the tool pegged the hard drive rather hard. It would be great to have the option to generate the webscene in memory (RAM), so that processing time would be cut down.
We're doing some pretty cool stuff with the CE Web Viewer and the new tool that exports ArcScene docs to WebScenes. The better the performance is, the farther we can take this tool.