Drupal's core pagination system does not scale well on large, high-traffic sites because of it's need to count the total number of items in the list. This involves wrapping the original query around a COUNT query like below.
SELECT COUNT(*) FROM (SELECT nid FROM node);
Count queries are usually very fast for tables using the MyISAM engine, but most high-traffic Drupal sites use the InnoDB engine for most of the tables.
