Wut? I train several football players, and some of them compete in the offseason. It's really not that much of a time commitment.
Also, going to 90 degrees doesn't mean anything. You could quarter squat and have a knee angle of 90 degrees, or you could be at legit depth...it all depends on where your hips are. But in my experience, squats to a box tend to inflate the numbers of most football players I've encountered.