The outside of the airplane has a forward-pointing tube called a pitot tube. As the airplane travels forward, air is compressed into this tube. By measuring the pressure, you can derive the airspeed. However the higher you go, the lower the ambient air pressure is and so the "indicated airspeed" is not at all accurate.
However indicated airspeed is still very useful as it measures the air resistance the aircraft is encountering which determines lift and airframe stresses (which is why the airframe speed limit is in indicated airspeed and not actual airspeed).
On the subject of indicated airspeed, does the mach number have the same meaning? That is, if the aircraft had reached an indicated airspeed of Mach 1, would they break the sound barrier and experience a sonic boom?
I think you have some confusion about indicated airspeed - it's used because it provides pilots with predictable information about how the plane will react, it's not indicative of the actual speed of the plane: https://en.wikipedia.org/wiki/Indicated_airspeed
They were truly at 0.9 mach, had they increased speed by 11% they would have broken the sound barrier, well before the indicated air speed would have read a >mach 1 number.
Indicated airspeed is not related to ground speed, but indicated airspeed is the important number, as far as keeping the aircraft in the air is concerned.
However indicated airspeed is still very useful as it measures the air resistance the aircraft is encountering which determines lift and airframe stresses (which is why the airframe speed limit is in indicated airspeed and not actual airspeed).