Sprinters can benefit from shorter leg to torso ratios because it enables faster turnover. Sprinters with longer legs seem to benefit from relatively shorter tibial length, again because it helps achieve faster turnover. Elite sprinters seem to have a wider range of leg lengths and ratios than distance runners. Andre DeGrasse has a long torso relative to his leg length. Bolt's legs are actually not particularly long compared to his upper body, it just seems that way because he is so large and angular.
In distance runners, having long legs and in particular having a longer tibia, confers an advantage. Compared to sprinters, distance runners employ more of a gliding motion while sprinters put down force and explode forward as quickly as possible. There is a very carefully conducted study comparing Europeans to Kenyans, that shows leg thinness, especially ankle thinness, to be perhaps the most important factor.
Western Europeans tend to have leg to torso ratios close to 1:1. Kenyans tend to be well over 1:1, usually 1.25:1 to 1.35:1 but can go as high as 1.5:1.
There are so many other factors at play in elite athletes, but all things being equal having thin legs and ankles and long legs will confer an advantage.
I don't think Van Niekirk's legs are short. Look at some of the photos of him training with Bolt.