Are you planning to use the onboard key manager or external?
I totally missed that while reading your post yesterday, sorry about that!
Not really any "gotchas" that I can think of with 9.3. But there are some out there in general, for example. upgrading ONTAP 9.1 to 9.3 they had users decrypt the their disks during an upgrade.
I would also test connection to the external key mangers during boot up too before you actually encrypt the disks.
And review the power guide before you start doing it. https://library.netapp.com/ecm/ecm_download_file/ECMLP2572742
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