This exactly, left handed people are known to have much more fun and generally be amazing great people, not speaking about anyone in general... So yeah that's most likely why, they know deep down Link is an awesome leftie and did this for him.
But being forced to hold the bow the wrong way makes it a pain to shoot, I actually had to use a guardian potion on Tentalus due to having horrible aim...
While it is true people usually pull the string with their preferred hand, which would result in Link using his right in Skyward Sword, the nunchuk is meant to be held with the left hand when playing. The motion control aspect allows for the nunchuk to be pulled back as if holding the string. It would be rather odd for the player to swing the left hand backward and Link does his right, no?
Link could always just be an ambidextrous fellow who prefers what isn't typical in a manner such as this. My dad holds a cricket bat with left-handedness despite using right for every other instance. Who knows what the case with Link is...