This reeks of communication. And what spot, not sure.
PDO appears to have generics compatible with DB2: http://ca2.php.net/manual/en/ref.pdo-odbc.php
, so I'd suggest you establish the connection via PDO to the DB2 db, and see how that goes.
If its still slow via httpd, I'd suggest that its definitely communication. Make sure you are working through local (assuming local yeah?) connections and not attempting to go offsite. Check the iptables, firewall or whatever you are using to block to make sure that its not being bottlenecked there.
If it fixes the problem, I'd suggest an issue in the odbc package itself. In which case I'd suggest not to bother with the odbc. I don't believe that the package is deprecated, but it is getting rather antiquated.
Typically you will see better performance on direct CLI, but not like 1/150th of a difference. More like 20% savings being normal.