Well, your wrists don't try to murder you if you keep them bent at an angle for too long, I suppose. Human hands are different, and mine really like having two separate controllers instead of holding just one thing.
But also, the JoyCons are pretty awesome, I find the separate button d-pad very reliable and I don't have a problem with the size at all, so even if they weren't healthier for me I'd love to have a set that works natively on PC.