I think you've misread my post: I do understand what balancing flash light and ambient light is, I do that quite a bit. I'm just saying for my applications, that is typically at night or in the late evening, the typical shutter speeds at typical ISOs (1600~3200) are 1/80 s~1/40 s (depending on the lens, the subject and the effect I'm going for). So what I am trying to say is whether the limit is at 1/200 s or 1/250 s doesn't matter much to me, because I rarely get close to 1/200 s when using my SB-600.
The D600's shutter shares many of the same specs as the D7000's shutter, and when you take into account that the shutter needs to traverse longer distances due to the difference in format, you arrive exactly at the max flash sync shutter speed: APS-C has a crop factor of 1.5x on Nikons which means that the sides are ~22 % longer (the square root of 1.5 is approximately 1.22). If you multiply 1/250 s by 1.22, you get roughly 1/204 s which is close enough to 1/200 s. That indicates that the D600 wasn't »neutered«, at least not in that respect.
So just assuming that the D600's shutter is a derivative of the D7000's shutter and taking the geometry into account explains why the max flash sync shutter speed is slower by that exact amount. You're right that with a different shutter (which is more expensive), you could achieve faster sync speeds, yes, but IMHO it's a trade-off that is worth it for most.