Low stances can injure the knees in particular if you're not doing them exactly right.
Being tense, and clenching the muscles around the knees can cause injury
Improper alignment of the knees in any stance can cause injury
Age is also an important factor. If you're older, and haven't trained for many years, you're unlikely to be able to attain low stances of any type past your 20's without joint injury.
But, while low stances in general are great for building strength, and can be used for more powerful strikes when one is less experienced, or for leverage, sinking into a lower stance after body to body contact has been made, high stances afford more upper body mobility, which is important for avoiding punches to the face, and allows a greater range of offensive techniques.
Low stances also reduce mobility in general, which is why you don't see them in combat sports or streetfighting.
(Note that boxers do not need low stances to knock an opponent out—they know how to use the body frame to root the feet and strike with maximum force from a high stance, and they're the best at that particular thing.)