This is more a medical question, not a historical one.

Medically, squatting to defecate is far healthier than sitting on a toilet seat. The puborectalis muscle forms a kind of sling around the lower end of the rectum, and in the sitting position, this sling is tightened, forming a kink in the rectum and squeezing it shut. This is why people don't normally leak feces while sitting on a chair. When people sit on the toilet seat, they consciously relax this muscle, but the kink in the rectum remains, and feces has to be forced past that kink.

This causes two problems: incomplete voiding, and straining. Straining eventually leads to hemorrhoids. And as you grow older, your muscles weaken and you can't strain as much, which worsens incomplete voiding. This is an aggravating factor for colon and rectal cancer.

Squatting straightens the anal canal, which allows voiding without straining. In fact, if you check out medical supplies stores for old people, you will find high footstools they sell to old people for use in the toilet. The idea is to sit on the toilet seat but put your feet up on this high footstool so your knees are up folded against your abdomen. It's as close to a squatting position as you can get while still resting your posterior on a toilet seat. This is recommended for people who have a hard time defecating.

Joint strain is not a problem if you are used to it (ligaments that have been stretched and toughened by squatting all your life can take the strain quite easily) and if you are not overweight. There are plenty of 70-80 year olds in Asian countries who have absolutely no problem squatting for extended periods. In fact, lacking chairs, many of them typically squat on the ground to do daily chores like cooking or laundry.

Unfortunately, I can't for the life of me inject some historical relevance into this to make it suitable for this subreddit. All I can say is that historically, everyone squatted to do his business, east and west. Perhaps some historian of bodily functions can shed light on when toilet seats became popular. I know (from having seen pictures) that Romans sometimes used communal toilets with holes cut in a plank at regular intervals as toilet seats. I am not sure how prevalent this was, though. I believe rural populations even then just went out mornings to squat and "fertilize the fields". Not sure when everyone in the west began sitting instead of squatting, but I'd think probably in the last 500 years or less.