So after studying what Microsoft has to offer about migrating Companyweb on SBS you'll find:
Interesting, it seems that the Microsoft procedure actually creates a second Sharepoint v3 site on the new SBS 2008 server. Quoting from the final results of the document:
You now have a working Windows SharePoint Services 3.0 Web site that is named OldCompanyWeb and that contains the structure and documents of your old Windows SBS 2003 CompanyWeb Web site. This is a good time to review the contents of your Windows SBS 2003 CompanyWeb Web site and to reorganize or archive items, if appropriate. You can open the new Windows SBS 2008 internal Web site and the Windows SBS 2003 OldCompanyWeb site side-by-side.
If you open document libraries and use the Explorer view, you can copy and paste documents and folders from one site to the other.
I must admit that if I had a really big Companyweb site I wouldn't want to be recreating it. It is fine to say "just copy the documents" but what about all the other information like lists, calendars, tasks and so on? I can see this being a pain even for a small site.
Now, I will admit I haven't verified that my method doesn't break anything and it may well do that (I think it may have issues with inbound faxes and maybe the database relocation wizard) but I will check those out as well as the suggest migration method from Microsoft.
On the other hand I can understand why Microsoft recommends doing it this way because who knows what customizations have been done to people's companyweb? Who knows if these will even migrate correctly? At least with a second Sharepoint v3 site if something "breaks" then you still have an original SBS2008 companyweb to fall back on.
So I can understand Microsoft's logic but if you have a big/complex SBS 2003 companyweb site and you want to take the Microsoft option then basically be prepared to recreate the site on SBS 2008 from what I see.