I rode dressage exclusively for nearly 4 months this year, complete with the dressage stirrup length. But I just went back to hunters -- and the shorter stirrup length -- and my knees and shins burned like crazy after the lesson, and sometimes even during. Thankfully, my trainer let me go up in small increments each week so my legs would have time to grow accustomed the shorter length. And sometimes, when I ride a different horse, with different girth size, my legs will do the same thing. (Especially going from a narrow horse to a wide one.)
Anyway, if you wanted to pursue the shorter length, or felt like you needed it, you could always get 1/2" hole stirrup leathers so you would have greater adjustability and you could ease them up or down a 1/2 hole at a time.
You may also want to think about different stirrup irons. Maybe some of those that flex and bend a bit to help absorb shock when you ride. In fact, I bought some cheap composite stirrups from Dover
recently, and they managed to take some pressure off my knees, even though they're not jointed. My dressage trainer also had 4-way flex stirrups I rode in that felt wonderful to my legs and knees.
I don't have any knee injuries, but I do have some occasional soreness that's no doubt from the years I played soccer and second-row in rugby.