I hope I answer all your questions:
1. In SPS 2003, the concept of workspaces are now available via Sites,
where each sites have their own web parts (Announcements, Discussion
Boards, News, Events, etc. for that specific site)
2. You can create one portal and have multiple sites. You only need
multiple virtual directories if you are creating multiple portals. But
from what you are describing below, you only need one portal with
multiple sites to accomodate your workspaces.
3. I think the limitation on the number of portals is 10 (somebody out
there might verify or confirm this, not sure)
4. You can access the various document folders via the web folder. With
SPS 2003, you can have infinite number of document libraries, it just
all depends on which document library you want to access because this
will determine the URL. If you are looking at dumping your current
documents into SPS 2003, each document library has an explorer view
where it supports cut and paste (you do this in IE). The only problem I
encountered when moving my documents was that it did not allow me to
move documents if there was an "&" anywhere in the name. But you can
move your documents using either the web folders or the explorer view.