Good info on "Ghosting"

Discussion on how opening/editing a WSS or SPS2003 site in FrontPage
2003 un-ghosts the site (places the site’s definition into the SQL
database instead of keeping the reference to the one on the server).
This can be very bad for performance!

SharePointU
discussion

Usage Analysis Tools in SharePoint Products and Technologies

Good TechNet article on how SharePoint uses access logs (it is
actually a chapter from the Microsoft SharePoint Products and
Technologies Resource Kit which you can find here:
http://www.microsoft.com/technet/prodtechnol/sppt/reskit/default.mspx):

http://www.microsoft.com/technet/prodtechnol/sppt/reskit/c2961881x.mspx

Why information is kept about users deleted from site collections

You can tell if the users have been deleted from the site collection
by looking at the UserInfo table of the content database. If the value
of the tp_Deleted column is 0, then the user is active in the site
collection. Otherwise, they have been removed.

SharePoint keeps this information around because it needs it to link
to the items placed on the sites. If it removed the users completely,
the items would become orphaned.