Does the speed of the air molecules matter in aircraft performance?
In some sense, yes it does.  But we usually don't think about it in those terms.  You usually only need to think about individual air molecules when the object you are talking about is very small.  For example, if you are trying determine the aerodynamics of an airplane whose length is 1/100th diameter of a human hair, then you might start caring about individual air molecules. For realistic sized planes, the planes are so big relative to the air molecules that we can just pretend that air is continuous. So instead of thinking about the motion of individual air molecules, we think about continuous variables such as density and temperature.  i.e. when your air molecules "spread out and faster moving" we say that is a higher temperature with a corresponding lower density, and when they are "compacted and slow moving" we say that is lower temperature and a higher density.  By doing that, we've taken the motion of a quadrillion individual air molecules and reduced it down to one single number. And that one single number, density, does have an affect on aircraft performance.  

For completeness, you also sometimes need to consider individual air molecules at very low pressures.  e.g. if your air pressure is a millionth of an atmosphere, then there are not many air molecules to go around and so each individual molecule's motion becomes more significant.  But airplanes generally do not fly at such low pressures.  Even at 40,000 ft, there's a lot more air pressure than that.