Hi,
Yes, you can use Encryption at Host with NVA just like with other VMs. Inside of the NVA VM it has no awareness that you are using Encryption at Host. It reads/writes to its hard disk as usual.
The above is subject to the documented restrictions of Encryption at Host, so if one of those apply to the NVA VM then you wouldn't be able to use it, but this is true for other VMs as well.
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Thanks.
-TP