It really depends on the details of what the file system does. It is true that older file systems did not encrypt metadata but that's not the case for newer one

It really depends on the details of what the file system does. It is true that older file systems did not encrypt metadata but that's not the case for newer ones like ZFS or APFS. The way I understand the scarce documentation about APFS is that all the metadata is encrypted with a disk key. But on top of that the file system encrypts user's files with a separate key. So just like block level encryption plaintext never hits the disk.