There are pros and cons for automatically snapshot after upgrade.
If you have different Junos on the partitions and something happens with the primary one, then you will boot from the alternate. Features that are available only in the primary Junos release will not be available anymore. More than that, if you have the EX in a VC, then it will stop forwarding traffic if the release is different.
But if you upgrade both partitions and then sudenly you have issues with the new release, you will need to rollback the upgrade. If the partitions have the old release and the new release, you could simply reboot from the alternate partition without going through the downgrade process.
What I suggest is to upgrade only one partition, keep the device running for some time(this will depend on you how much is relevant to draw a conclusion) and then do a snapshot to the other partition.
You might consider this once you have both partitions with the same release:
http://www.juniper.net/documentation/en_US/junos12.3/topics/reference/configuration-statement/auto-snapshot-edit-system.html
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