Encrypting user data is pretty standard in the industry, and even required by law in the instance of servers hosting medical information in the US. Consumer software for disk encryption like you mentioned is substantially different from usual encryption solutions employed by data centers. Whole disk encryption is commonly done at a firmware or hardware level. For an example, iPhone embedded storage is fully encrypted and tied to the rest of the phone’s hardware. No user input required.

It wouldn’t have mattered if the guy had encryption any way because, as the article mentioned:

To make matters worse, it appears that the admin targeted in the raid was in the middle of maintenance work which left would-be-encrypted material on the server available in unencrypted form at the time of seizure.