A few studies have shown that the parallel squat is king for maximizing work and overloading on the muscles . High reps with low to moderate weight gives exercisers the least effective way to overload the lower body muscles. The deep squat can contribute to tight knee joints / kneecap pressure . With this in mind , would you put deep squats in your personal leg workout ?
I personally prefer the Goblet squats (w/ kettlebells or sandbags) and the pistols (one legged squats using a weighted plate, kettlebell, dumbbell or sandbag) than the traditional squats with the bar. As for when I train my clients, it depends on their fitness level, flexibility and/or any injuries they might have.