Yes. And if you then put that drive in a computer as the primary drive (it's not just a data drive), you'll have a 500GB drive minus whatever space is needed to load an operating system. Doesn't matter if it's Windows, Mac, Linux, etc. That operating system needs to live somewhere. And in this case, that "somewhere" is the free space on your drive.
The phone is no different. They just come with the OS already installed for you.
Maybe this is semantics, maybe not. If you buy a bare drive, you get what you paid for. If you buy a computer with an operating system installed, the storage capacity available is net of the space required for the operating system. I think that's the correct analogy to the phone.
As I said. It's a small thing that bugs me on rare occasions. It really doesn't need in depth discussion and over analysis.