The reason is twofold.
Firstly, hands are traditionally struck with what is perhaps best described as a very simple ‘vertically downward’ motion, whereas bottoms are usually struck in a more complex essentially horizontal manner which allows much greater force to be used.
Secondly, hands are significantly more fragile than bottoms and there is therefore a relatively very low limit to the force that may safely be used when striking them.
Given the above, and given that hand strapping/caning is rarely described as being less than very painful, it would appear that, other things being equal, it IS fundamentally more painful than taking it on the bum.
In practice, however, other things are NOT equal and the fact that so much more force may be (and usually was) used on the bottom means that, inevitably, many bottoms suffered more than hands.