I forked over the money for their repair. Now let's see if I get my system back with the 1TB HDD that I put in it. Heck, let's see if they fix it at all.
Edit: Also, having just looked up PS4 failure rates being at just under 1%, I'm a little more confident in their hardware.
Well the only scenario I see where you would not get your 1TB back is if they decide to give you a new PS4, and forget to give back the drive. Otherwise you should get your system back the way it was.
I was thinking that a new PS4 costs 200, but it's probably more than that unless there's a deal of some kind. So 99 to fix it may be the better choice.
I haven't looked up failure rates so I can only go based on myself and people I know, but I'm not aware of any friends needing to get theirs fixed (although one friend had an issue with a controller, until he bought a new controller) so hopefully it was a one time thing and you won't have any issues again.