I eliminated weighted squats because they were affecting my athletic performance. They made me tight and stiff, especially upper hamstrings right below my glutes. I was worried I would lose strength at first but I ran and jumped so much better I eventually didn't care.
The other thing I worried about was injury, but I still do body weight squats and lunges and I'm going on 4 years now of not programming weighted squats(after squatting 2-3 times a week for 7 years). Once in a while I'll squat to see if I'm losing strength. I almost think I am stronger. Granted my PB squat was 335x5, at 165 lbs, so I'm nowhere near elite, but I can still work up to 315 for reps whenever I want. I figure all the force production and ab work from sprinting and jumping is keeping me where I was.
Anyway, everyone is different.