Yes, Tomcat does use Apache DBCP pooling by default for DataSources defined as JNDI Context resources.
From documentation at
http://tomcat.apache.org/tomcat-7.0-doc/jndi-resources-howto.html#JDBC_Data_Sources
NOTE - The default data source support
in Tomcat is based on the DBCP
connection pool from the Commons
project. However, it is possible to
use any other connection pool that
implements javax.sql.DataSource, by
writing your own custom resource
factory, as described below.
Digging Tomcat 6 sources revealed that they obtain connection factory this way (in case when you don't specify your own using Context's "factory" attribute):
ObjectFactory factory = (ObjectFactory)Class.forName(System.getProperty("javax.sql.DataSource.Factory", "org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory")).newInstance();
And org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory that implements javax.naming.spi.ObjectFactory takes care of creating DataSource instances:
http://www.jarvana.com/jarvana/view/org/apache/tomcat/tomcat-dbcp/7.0.2/tomcat-dbcp-7.0.2-sources.jar!/org/apache/tomcat/dbcp/dbcp/BasicDataSourceFactory.java?format=ok
I see they create instances of org.apache.tomcat.dbcp.dbcp.BasicDataSource:
http://www.jarvana.com/jarvana/view/org/apache/tomcat/tomcat-dbcp/7.0.2/tomcat-dbcp-7.0.2-sources.jar!/org/apache/tomcat/dbcp/dbcp/BasicDataSource.java?format=ok
Oddly enough, this class doesn't implement ConnectionPoolDataSource itself, neither does org.apache.tomcat.dbcp.dbcp.PoolingDataSource, that's returned internally by BasicDataSource
http://www.jarvana.com/jarvana/view/org/apache/tomcat/tomcat-dbcp/7.0.2/tomcat-dbcp-7.0.2-sources.jar!/org/apache/tomcat/dbcp/dbcp/PoolingDataSource.java?format=ok
So I presume when you configured your DataSources as javax.sql.ConnectionPoolDataSource you also used some custom-defined factory (it's just a guess, but I suppose otherwise you'd have class cast exceptions in Tomcat, since their pooling doesn't really provide instances of javax.sql.ConnectionPoolDataSource, only javax.sql.DataSource).
Thus, to answer questions about advantages or disadvantages of particular case you should compare Apache DBCP against pooling mechanism in your DataSource factory, whichever one you used.