I have my sprinters do almost all of my speed work in spikes. The only time they aren't in spikes for speed work is EARLY in the year or if they have some type of lower leg injury.
As for being bad for the knees, I've actually never noticed this to be the case. I've seen stress reaction type injuries in the foot and tib / fib but never in the knee. In these cases it was almost always because the jump to speed work in spikes had been too sudden or inappropriately (like when coming back from a different injury).