The next major release of Drupal (7) has a fair number of improvements towards semi-automated maintenance and upgrades.  Most of these leverage off a command line interface called drush.<p>Also, Joomla, Drupal's closest analog, has a comparable number of DB tables per site.  The problem is more likely with prevailing conventions in certain open-source CMS design, than with a particular CMS.  Drupal at least lets you share strategic tables across multiple sites.