Can AIM wavefunctions derived from calculations using Spherical Harmonic / Pure (in other words 5D, 7F, 9G, 11H instead of 6D, 10F, 15G, 21H) Gaussian basis sets be used?
Yes, as long as the Pure Gaussian basis set has been properly converted to the equivalent Cartesian Gaussian basis set when the AIM wavefunction is created. This conversion is done automatically by AIM wavefunction writers. The definition (which is used for historical reasons rather than logical ones) of the Cartesian Gaussian primitive type numbers appearing in both traditional AIM .wfn files and extended AIM .wfx files is given here.