Let us talk about two variants of Squats, the Front Squat and the Back Squat.
The Front Squats are Quad Dominant. And your knees will definitely go well past your toes. Owing to the fact that the hamstrings are very shortened in this Squat, they do not contribute towards any hip extension.
The Back Squat, at-least in the Low Bar Back Squat, where the Hip Drive forms a very important component, the Posterior Chain of Muscles (the hamstring, the glutes and the lower back) contribute quite heavily towards Hip Extension. Here, the emphasis is on Hip Drive. However, here too, the knees will go past the toes, but only just a bit. Exactly how much, depends on an individual’s anthropometry, but it is nowhere as much ahead of the toes, as in the Front Squat.
There is a myth that allowing your knees to go past your toes in any manner at all, will cause knee damage and hence knees must never go over your toes in any version of the squat. Well, just make sure to follow proper mechanics for each of the squats, and ensure that weight stays mid-foot and does NOT lean forward/drift towards your toes. Ensure that the toes are turned out to allow for proper opening of the hips (which in turn, allows for a proper lower back extension). The knees must ALWAYS keep in line with the toes…this is VERY IMPORTANT.
With all the above, performing squats (all variations) are very good for you…the knees will drift forward of the toes, but, must happen in an appropriate manner, as discussed