Can too much jumping hurt a toddler's knees?
Yes, like too much of anything (even water) can hurt someone, too much jumping can hurt a toddler's knees, hips, and what not.
An animal model of this phenomenon is appropriate here: exercise and hip disease.
...Many breeders will advise against exercising a pup to prevent the development of orthopedic conditions. Nonetheless, veterinarians believe that gentle, low impact exercise can be beneficial for pups, but that all forced exercise beyond what a puppy would normally do should be avoided. Veterinarians maintain that running should be avoided until a puppy is physically mature, and that puppies should stay away from high impact sports such as jumping and agility. Both of these activities are believed to be traumatic on a puppy's immature joints.
This really came to light in a big way when agility became a leading competitive sport for dogs. People started training their dogs at way too early an age. But please note that dogs don't jump hurdles repetitively at an early age for the sheer joy of it. Unless the dog has a breed-specific proneness to injury (such as Corgies), letting a puppy do whatever a puppy likes to do (they'll avoid what hurts) is just fine. It's when people come into the picture pushing inappropriate exercise onto them that puppies can become injured, sometimes for life.
Likewise, a toddler doing what he loves to do safely (no open windows around, unguarded stairwells, no sticking objects small enough to choke him in his mouth, etc., etc.) will not sustain major or lifelong injury. A baby/toddler will stop doing something when he's had enough. If, however, you forced your son to jump off the last two steps of every stairway he encountered day after day, I'm pretty sure some lasting damage would be done. Few right-minded parents do this with toddlers.
This is not to say kids don't overdo things that aren't so good for them physically. Certain baseball pitches in Little Leaguers caused permanent damage in Little Leaguers (adolescents) in the US a few decades back. Knee injuries among high-school (American) football players are common. But average toddlers usually aren't motivated to incur repetitive use syndromes.