Backup SQL encrypted databases

Yes, your specific setups are supported:

• Standard VMware agentless backups of SQL VMs in an Always On Availability Group, with Application-Aware Processing

• Windows Agent backup jobs across the cluster nodes, with Application-Aware Processing

Both configurations are fully compatible with SQL databases encrypted using Transparent Data Encryption (TDE) or Always Encrypted, since Veeam uses native SQL Server backup APIs.

The only caveat, in case you decide to use the native Veeam plug-in for Microsoft SQL Server (instead of the methods mentioned above), is that:

• Databases using TDE do not support compression when backed up via the plug-in

• Differential backups are not supported on secondary replicas

However, this limitation does not apply to the two scenarios you mentioned (agentless VMware and Windows Agent with Application-Aware Processing).

You can see more here.