Most boats have hand controls and jetboats mostly have foot throttles, how weird would it be to have the throttle against the hull sides (gunwale)?...
The other reason is, with the driver on the right, the hand control seems more natural, you can do it with the left hand but it seems wrong....This mostly started because a large majority of early boat builders (not companies, but craftsmen who built boats the "old fashioned way") hailed from Europe, where the drive on the left side of the road...

Torque had a little to do with it in the early days on outboards, but not really too much on inboards or vee drives and they have been around much longer than the lowly outboard...(that did not have tiller steering that is) yet the inboards have had them on the right for decades.
The other reason I have heard was for navigation purposes, the marker buoys were "read" from the right....Ever heard "red right on return"? That one came from my grand dad and at the time made total sense....

Lakes and rivers sort of made it seem wrong because of the counter clockwise rotation law, it was done that way because of the road rules of driving on the right, they figured people were not smart enough to figure out if it was clockwise, something I happen to totally agree with....

GT