Yup, that's how Harddrive work. 500 GB is really around ~ 465 GB (in real computer terms).
Hard drives are always measured as if 1,000 KB were in a MB, 1,000 MB were in a GB, etc, when in reality 1,024 KB are in a MB (to any computer and devices) and 1,024 MB are in GB. Thus, accounting for part of the discrepancy. As for the 408 GB usable space, the remaining is most likely the OS plus any additional firmware or default installed applications. From this, we know that out of the box the PS4 OS plus it's firmware, plus it's pre-installed applications (that one cannot removed) comes to around 57 GB, which is quite large.
I have been saying this in other threads (particularly the various PS4 "caching" threads), 500 GB is not enough space if every game utilizes their "caching" solution. As we can see, 3 games have utilized ~84 GB (minus some for other downloaded applications like Netflix and such, but this is most likely +/- 5GB). Thtat's a lot of space, and we are going to be running out of HD space very, very quickly. And I thought Wii U was bad with 32 GB. At least there I can choose to buy retail and save space.
EDIT: See Shadow Hog's post directly below this for even further clarification.