From what I know, on lighter sets you should by all means ensure you reach the bottom of the movement as it ensures you hit every possible fibre whilst strengthening the surrounding musculature to support at that range HOWEVER when going heavy it is not wise as it can tax joints quite badly
What do you mean by lighter sets? Higher RIR (further from failure),warm up sets or just generally lighter weight like 7-10-15kg? How it taxes the joints exactly? It only applies to monoarticular exercises or also to an exercise such as the squat where it is usually recommended to go as deep as possible?