Will Hyper loop succeed as a means of human transportation? What would be the adverse effect on the human body travelling at 1000km/h?
No impact at all as long as you don't open the window. The effect of ~500 mph wind (~800km/h) on someones face can be seen here: https://www.youtube.com/watch?v=IU4SDDNXuUA .
Someone in the space station will be going a lot faster than that (about 27,600km/h) and they have a nice smooth ride (and even bigger problems if someone opened a window). The rough bits are getting there and back, they have to accelerate up to those speeds and then slow down again.
If you assume that the air the person is breathing is moving with the person then speed isn't an issue but acceleration is.
The acceleration to get to 1000 km/h and slow down again could have an impact but it only needs 1g for 30 seconds. 1g sitting down and sitting facing forward isn't excessive. Slowing down would have to take longer unless you somehow rotated the seats so that you faced backwards for the braking. It's one thing to be pushed back into a chair, it's another to be thrown forward.
The other big issue is bumps or corners in the track. At those speeds it doesn't take much of a bump to result in large accelerations, similarly any corner will have to have a massive turning circle to avoid excessive lateral forces. You need a very smooth track to avoid it feeling like the worlds largest rollercoaster.