I just gave the 80% saturated number as an example. The truth is, if you have hard water, your water is probably very close to 100% saturated. So any boiling/evaporation will leave some limescale. The amount you boil off is probably more than you think, 0.01% is not right, even if you take the water to just boiling and stop, it has probably lost 2,3,even 5%. Also, you only deposit a tiny amount of limescale mass each time, it adds up. You don't get the huge amount of limescaling after the first use. There is a tiny amount -- but you cannot see it. A big culprit is also people leaving water in the kettle. Water evaporates slowly over time, which again always leaves a little bit of minerals. All this adds up.
Yes, you can boil off the CO2, but the CO2 comes back. Rather quickly, too, especially in a fishtank where the water is circulated. That same circulation that provides good oxygen exchange at the surface also provides good CO2 exchange. Just letting the water cool after boiling will also bring the CO2 back in. So, unless you did a very large water change, like 75% or so, with water that was just boiled and not allowed to sit out, the KH will be back to it normal standard pretty darn quickly. Even then, the circulation of the water in the tank will be restoring the KH. At the beginning, when the water has very little CO2, the CO2 will enter the water very rapidly, it is probably only a matter of a few minutes before at least half the KH is back, maybe more. I agree the water will lose KH temporarily, but it will get back to its normal level rather quickly. That water retains is buffering capability once the CO2 comes back into it.