I note that by "heavy" I assume you're meaning relative to the individual's strength. I don't claim to know about 300kg squats, I'm talking here about the typical person I have coming to my gyms, where it is rare to see a twice a person's bodyweight on the barbell.
I have heard of the dangers of deep squats many times, including from exercise physiologists. None have been able to tell me exactly the nature of the injury risked by deep squats.
I can tell you about the injuries risked by bench-pressing, by improper deadlifting, by "power curls", by kipping pullups, and so on. And exercise physiologists and the like can tell us in greater detail than me.
But nobody can tell me exactly what bad things are supposed to be happening to the knees during deep heavy squats. They start talking about forces etc, when I ask which muscle or ligament is going to tear, they cannot tell me. Nor can they give examples of healthy individuals who have been injured while performing deep squats with correct technique.
In gyms I get many people come to me, I say, "we'll start you out with a simple bodyweight squat, let's see how you do it."
"Squats hurt my knees."
"Show me how you squat."
They stand with feet shoulder-width apart, kneel down onto their toes, and their knees collapse inwards. Since they're bending their knee in a way it's not designed to bend, I'm not surprised it hurts. I then teach them correct squatting technique and it's almost alway okay - the only exceptions so far have been one guy who'd had a botched knee reconstruction and the femur and tibia were in direct contact, and another guy who had arthritis.
As for how deep to go, I would observe that sitting in a parallel squat position against the wall is used as a punishment in the military, whereas sitting in a deep squat is done every day by about 3 billion Asians and Africans.
The parallel squat causes pain, the deep squat is used as relaxation. In general, pain is the sign of an increased risk of injury, that's the way our bodies work. So I say: go deep.
It's quite right to consider a person's goals when thinking of which exercises to perform, and how to perform them. Looking at the typical gym-goer we have to consider first of basic health. Good health is the basis of good looks and good performance. So what about the health of the beginner? Our bodies don't only adapt to what we do in the gym, but to our day-to-day lives as well. Our Western society is a seated society, we sit down for work, sit down for transport, and sit down for leisure. Our bodies adapt to that. Our hamstrings are unused but tight, our glutes and abdominals are unused. As a result we get anterior pelvic tilt, lower back pain, torn hamstrings in sports with vertical jumping, and so on.
So the problem is that our abs, glutes and hams are weak. Abs are a postural muscle, best worked by maintaining posture - if you can stand up straight with even 40kg on your back, you can stand up straight with no weight. As for glutes and hams, they are hip extensors - they straighten the leg at the hip. In a bicep curl, the biceps are worked more going from straight out to bent right up than those half-curls you see. Likewise, the more the hip is flexed the more the glutes and hams are worked.
Tight hamstrings will also be more loosened by a deep squat than a shallow one. I have a client who began at 165kg bodyweight, with no stretching except a few times after a workout to lessen DOMS, he has improved his mobility so that he can now touch his toes. How? Deep squats.
Thus, deep heavy squats will strengthen the muscles made weak by our Western seated lifestyle, improving our posture, and improve joint mobility. Parallel squats will not strengthen nor loosen those muscles as much. Deep squats mean we use weak muscles. This is why most people avoid deep squats - they're bloody hard. They would rather use their strong muscles than their weak. Thus the legions of bench press and curlz boyz in the gym.