I think human audio capabilities reach up to 20,000khz so I wonder if the difference can really be noticed when listening, although, mathematical there is a difference in audio...but it's hard to distinguish, especially if audio has been re-sampled in emulation. I have problems with timing in emulated audio, that is, when making tracker songs, emulation does not seem so accurate or 'punchy' as it would do if it were played on a real Amiga.
There are delays in replayer routines you dont really notice but when played in faster Amiga you notice it sounds slightly different. It is very subtle but it is there.
