It seems the core question is "is there any disadvantage to encrypting my S3 objects and EBS volumes"?
Factors:
- You have to be careful not to delete your encryption keys or you'll lose access to your data, unless they're AWS default credentials.
- Encryption might add a tiny bit of latency - though not much as I suspect it's done by Nitro hardware in the latest gen instances.
All in all there's no significant disadvantage that I can see.
There's also not much of an advantage - encryption at rest primarily prevents people accessing your data if they steal the storage device, and that's not going to happen in an AWS data center as they have good physical security and securely destroy devices that are disposed of. However, using Customer Managed Keys and a Custom Key Policy does have some advantages.
Update
As of 5 Jan 2023, S3 objects are encrypted by default. As I mentioned above, this doesn't really help security all that much because AWS has the decryption keys and decrypts the objects when a valid request is received for the objects.