The eastern practice of aligning the chakras has to do with the energy of the universe as it funnels through the physical body. This energy is manifested in various parts of the body and aligning it just means paying attention to ensure that the various energy centers are working as they should, giving a person more well being.
Even if you don't understand what chakra are or how to align them, the study of the metaphysical can only lead to an enhanced awareness of your body and your spirituality. And this enhanced awareness is bound to make you healthier, as you pay better attention to what you eat, how much you eat, your exercise and sleep habits, and other activities that contribute to or take away from good health.
I believe the proper chakra alignments can lead to better overall health. This is not a notion that is discussed often in American medicines or even alternative medicines but I do think it can be beneficial. I think the chakra system promotes mind over matter, which can help people in the end.
No, I believe that these so called knots in the body and joints do not lead to better over all health if they are aligned or not. Most people will spend their whole life with no pain or medical problems that occur from these things being out of line in the body.
It means nothing. Chakras, while in traditional Hindu culture, are not medically based in scientific fact. The methods of Chakra alignment, specifically the way people are supposed to live and the physical practices (yoga, healthy sexual activity etc.) are definitely healthy, the chakras part of things itself is not effective.