The figure of 2000 items (now 5000 for SharePoint 2010) is a recommended maximum for a single view, i.e. showing them in the browser, and is called the list view threshold. It is a well-known myth that in earlier versions of SharePoint there was a 2000 item limit for lists - in fact this was never the case.
The current recommendation for SharePoint 2010 is a maximum of items per list or document library of 30,000,000 (yes, 30 million). There is no specific limit on the number of document libraries per site that I am aware of, but bear in mind that there is a recommended maximum storage size of 100 Gb per site collection. In practice I think a large number of document libraries in a single site would become impractical to manage in the administrative interface before you reached any performance-related limit.
Technet guidance (SharePoint 2010):
The Technet guidance for SharePoint 2007 is unfortunately widely misinterpreted. Although it does now state that the "2000" figure refers to built-in UI performance, you have to read it very carefully. Many people over the last few years have referred to this document and been left with the impression that SharePoint has a limit of 2000 items in lists, document libraries etc. Probably the best explanation is at http://www.binarywave.com/blogs/eshupps/Lists/Posts/Post.aspx?ID=188.