Dave, being well-educated, is of course right.
Well-performed squats will be good for knees which are healthy to begin with, strengthening the muscles around the knees, taking pressure off ligaments and so on.
Cracking sounds are not necessarily indicators that injury is about to happen, or the movement is dangerous. That's just human bodies, there are so many tendons and so on crossing each-other and jostling for space next to each-other that all sorts of bits and pieces can be sliding over each-other making funny noises. So that's not a concern.
Pain is a concern, especially if it's pain which comes consistently with a particular movement, or which remains day-to-day. If that's the case, you should definitely see a sports physiotherapist.
Odd little aches and pains that come and go and are not associated with particular movements, this is what people have when they're sedentary, when they spend more time sitting on their bums in front of computer or tv screens than they spend up on their feet and doing physical stuff. Many people find that these odd little aches and pains with no consistent cause entirely disappear once they're physically active.