Hard surfaces like concrete DO hurt the knees - after all, they’re not a terribly well-cushioned part of the body! And concrete is usually fairly cold, so that would make it more painful.
And merely staying in any one posture, whichever it be, for a long time will be uncomfortable. The human body is designed not to stay in one posture for a long time, but to move and shift around. Even while people are asleep they will keep shifting their position from the back to side or stomach, or move around in other ways.
As for the nausea - because your knees are bent by your kneeling, and pressure is being put on your skin by the contact with the floor, your circulation is actually being cut off, at least a little bit. That might cause some light-headedness (you aren’t getting enough bloodflow to the brain) and nausea which can go with it.