While the space wasted by GPT and partitions and by the arbitrary alignment rules used by various formatting tools is not great, I do not see any reason why it should exist. The space wasted now with GPT and UEFI is several orders of magnitude greater than it was with traditional partition tables, so eliminating it has become more attractive.
Such SSDs and HDDs are not bootable, but for me this is a desirable feature, not a bug. I boot my computers either from Ethernet (e.g. most of my servers) or from a removable USB memory.
The SSDs and HDDs with a whole-disk file system are also wholly encrypted. As in a proper encryption implementation, there is complete separation between the encrypted data and the encryption key. The encrypted disks or their hosting computers do not contain any information about decryption, unlike in many systems of disk encryption. The encrypted decryption keys can be found only on external or remote boot media, which are not normally associated with the hosting computers.