The hypersonic speed is triggered as soon as the booster stage is released and the scramjet starts working to achieve those speeds. I believe the Russians know that the determining factor of Tsirkon is not its description of avoiding detection by enemy systems, but its speed. Hypersonic speed means it must fly relatively high, which means it must be able to be detected at long range, but the high speed will reduce the available reaction time and, of course, the maneuverability would make it a desperately difficult target to be engaged.
Traveling at high altitudes is not a problem because the very high speed means that although the air may be cooler and thinner, the volume of air collected is huge simply because of the flight speed, so it's okay to use a scramjet engine. In reality, the scramjet engine works best at high altitude, so staying at high altitude and diving to land on the target can be a useful concept. Tsirkon will fly at mach 8 only at high altitudes. At high altitudes the air is less dense compared to lower altitudes. The heat accumulated due to friction with the air will be less at these higher altitudes, at which altitude the scramjet will work best, so the Zircon would hardly perform any flight course action at low altitude.
Plasma is created around mach 6 and becomes increasingly detrimental to radio communications thereafter. On mach 8, signals such as GPS reception will be seriously affected.
As for temperature, hypersonic velocities generally generate boundary-layer temperatures of 1000°C or more, enough temperature to saturate the IR sensors, that in itself is not a problem, the Tsirkon probably at terminal velocity, will have speeds at mach 6, SAM missiles like the Russian 48N6 has 6.2 mach speed and even features a semi-active nose radar.
Going back to the IR sensors issue, behind a nose blinded by the plasma, the Tsirkon missile may have forward-facing side IR sensors that it might be able to look even under the plasma. In addition, a normal old technology cooled thermal imager has its elements cooled with liquid nitrogen, cooling the surface of the missile. To overcome the problem of generated heat, Tsirkon can easily have ablative materials near the hot spots (nose) and even pump its liquid fuel through the surface of the skin where heating occurs to prepare the fuel and cool the surface.
Regarding the search for the target, it all comes down to how much the target moves and how accurately the target is located in the first place, it is worth noting that the missile flying at mach 6, will reach the target in less than 7 minutes at 500 km from range, compared to the target ship, it will travel a much shorter distance in any direction, leaving a much smaller target area for the missile to search for the target. Just noting that most ballistic targets when performing the maneuver reduces speed, but for Tsirkon which is a powered missile, then it won't lose as much speed during turns, and can regain lost speed, in the matter facing Tsirkon, slow down speeds before hitting targets is due to target acquisition, last stage tracking, with the scramjet engine burning all the time means more energy and the ability to maneuver without necessarily losing speed.
