I'm not sure about why that's the standard, but it may have to do with the fact that in fighting games you don't want to be jumping all the time, it's something that you have to do carefully, while crouching is something you do constantly, and most motion inputs involve the "down" direction (like quarter circles or the shoryuken input), and having left-down-right lined up makes it pretty easy to do those motions. Think about pressing your Q-W-E keys in quick succesion. You can probably do that without much practice. That's a half-circle-forward motion. If you have "down" in your thumb, a half-circle would be like pressing "Q-Spacebar-E" in quick succesion, which is more difficult.

Maybe it's also because people often use the space bar in keyboards to jump in many games, and that's what they were used to.

In any case, once you get used to this layout, it's very comfortable.