The highest audio tone that can be captured is very slightly less than one-half the sampling rate of an analog-to-digital convertor.
So the 22khz rate will not save sounds much above 10kHz and will result in music missing the highest harmonics,whereas 44(actually 44.1kHz) sampling will save all the sounds even the best human ears can hear,that is up to 22kHz.Most people lose the hearing of higher pitched sounds as the person ages,especially if exposed to lots of loud sounds.
But how anyone can compare sampling a digital joystick to sampling analog audio, is beyond me.
With audio, its quite obvious that capturing as much accuracy as possible, especially during mixing/mastering, is useful. The more accurate data you have, the more accurately you will be mixing it. So that once you drop it back down to 44.1 or 48Khz, you are getting a better approximation. Thats just plain maths, the more precision the better the more accurate the result.
Now a digital Joystick? Nobody has yet explained how being able to tell what happened to the joystick between screen refreshes actually has any bearing at all on a game. Yes sampling quicker is more accurate, nobody every denied that. But accuracy is only any good when its actually useful.
A mouse its useful to sample quicker, the electronics can counteract any questionable result that way (especially led/laser mice, you could get a rogue reflection from dust, a crack, poor mouse mat) and most of all - there will be less lag from the mouse itself.
Just look at LCD TVs. The biggest lag on an LCD TV is not the pixel response time, its how quickly the TV can process the signal and actually tell those pixels to change. That is one reason why a cheap TV and an expensive one often can be really different, even if they are using the same LCD panel.
So yeah, the Amiga joystick port is fast, and it might be useful if you are using it for some custom purpose rather than a joystick. But then if you are going that direction why use such old technology when you could just use a modern PIC using far far less electricity. I mean its a silly argument as there are things the Minimig can do that neither the Amiga nor PC can do, but that does not mean PC is trying to catch up to it.