The hamstrings don't just do the knee flexion movement, they also do the hip extension movement, which is present in the squat.
So, the hams can extend the hip and flex the knee, but you can't really choose which one of the functions you want as far as I know. If the muscle contracts, it contracts. So if it contracts in a squat to give you hip extension in the concentric portion, the activity in the hams will also act on knee flextion, which you don't want, you want knee extension! So the hams would be working against the movement at the knee. I think this is the reason you don't see super high hamstring activity in the squat, the body probably inhibits it and relies more on the glutes for the hip extension since the glutes won't counteract the knee movement.
Another, more simple, reason (probably working in concert with what I wrote above), could be that as the knee flexes in the eccentric part of the squat, the hamstrings will become "slack". although the hip flexion in the eccentric part will counteract this somewhat, with exercises like RDLs you have almost no knee extension and a lot of hip flexion (at the bottom of the movement) meaning that the hams are not slack, but "****ed" and ready for action. One of the reasons you see people popping their butts up first out of the hole in a squat (called GMing out of the hole) is because that will stretch the hamstrings making them more active, which will help them to get the bar up (the hams are a big and strong muscle group)
I'll see if I can find any studies on hamstring activity in the squat, but I'm almost 100% sure it's there, but probably not enough to develop your hamstrings to their fullest potential. I've found a lot of abstracts, but I'm not at the uni now so I don't get access to full texts