A new update is out since a few days for Systems Director (here are the new things : http://publib.boulder.ibm.com/infocenter/director/pubs/index.jsp?topic=%2Fcom.ibm.director.main.helps.doc%2Ffqm0_r_whats_new_in_release_631.html ) and the update method is quite simple !

root@ISD_server /tmp #> smcli installneeded -v /opt/SysDir6_3_1_AIX.zip
ATKUPD489I Collecting inventory for one or more systems.
ATKUSC206I Generating SDDs for path: "/opt/SysDir6_3_1_AIX.zip".
ATKUSC206I Generating SDDs for path: "/opt/ibm/director/data/updateslib/TEMP0786411300026836".
ATKUPD293I Update "agentmanager.feature_6.3.1" was successfully imported to the library.

[blah blah blah...]

ATKUPD293I Update "com.ibm.vmcontrol.vim.help.doc.feature_2.4.1" was successfully imported to the library.
ATKUPD293I Update "org.sblim.cim.client.feature_2.1.2" was successfully imported to the library.
ATKUPD573I Running compliance for all new updates that were found.
ATKUPD286I The import updates task has completed successfully.
ATKUSC209I The install needed task found updates that need to be installed for system "ISD_server":
 com.ibm.director.core.manager.aix_6.3.1
 com.ibm.lwi.activemq.feature_8.1.1.1-LWI
 com.ibm.lwi.eclipse.help.feature_8.1.1.1-LWI
ATKUSC210I This operation will install the updates listed above. To continue, type "1" for yes or "0" for no.
1
ATKUPD725I The update install task has started.
ATKUPD487I The download task has finished successfully.
ATKUPD629I Installation staging will be performed to 1 systems.
ATKUPD632I The Installation Staging task is starting to process system "ISD_server".
ATKUPD633I The Installation Staging task has finished processing system "ISD_server".
ATKUPD630I The update installation staging has completed.
ATKUPD760I Start processing update "com.ibm.lwi.activemq.feature_8.1.1.1-LWI" and system "ISD_server".
ATKUPD764I Update "com.ibm.lwi.activemq.feature_8.1.1.1-LWI" was installed on system "ISD_server" successfully.
ATKUPD760I Start processing update "com.ibm.director.core.manager.aix_6.3.1" and system "ISD_server".
ATKUPD764I Update "com.ibm.director.core.manager.aix_6.3.1" was installed on system "ISD_server" successfully.
ATKUPD760I Start processing update "com.ibm.lwi.eclipse.help.feature_8.1.1.1-LWI" and system "ISD_server".
ATKUPD764I Update "com.ibm.lwi.eclipse.help.feature_8.1.1.1-LWI" was installed on system "ISD_server" successfully.
ATKUPD795I You must manually restart the IBM® Systems Director management server after this install completes for the updates to take effect.
ATKUPD739I Collecting inventory on system "ISD_server".
ATKUPD572I Running compliance on system "ISD_server".
ATKUPD727I The update install task has finished successfully.
ATKUPD288I The install needed updates task has completed successfully.

Now we need to restart ISD in order to apply the update :

root@ISD_server /root #> smstop && smstart && smstatus -r
Shutting down IBM Director...
Starting IBM Director...
The starting process may take a while. Please use smstatus to check if the server is active.

Error
Starting
Updating
Starting
Active
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IBM Systems Director : Updating from 6.3 to 6.3.1 with smcli
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