I wouldn't create a new portal site for each workspace. You have a group workspace you mentioned and that really aligns to the main portal site. Each separate workspace you have now (Finance, Marketing, Sales, etc.) would be a site underneath the main portal site. You can either use the team site template or construct your own and then add each department through the Site directory. This way your users can search the sites at the portal level and navigate down to the one they're looking for. We have a similar setup here with 150 projects under one workspace in V1 that I'm migrating to a single portal site with 150 team sites (customized) for each project.

You may want to look at the CorasWorks webparts and/or project workplace (www.corasworks.net) as they allow you to put a navigation tree on the main portal site and will let your users navigate down (up to 10 levels) so if you have a lot of depth you might want to consider this as it eliminates the need to know what site belongs to what parent site (if you have multiple levels).

As for accessing via web folders vs web, you'll find with SPS 2003 that the web is very fast thanks to ASP.NET.

Hope that helps.