I agree with your mother that if your kilt has belt loops, they should be sewn on before the top waist band, with the waist band covering the top of the belt loops -- and this is how I make them, when I get requests for them.

But all other arguments about "adversely affecting the hang of the pleats" aside, there is one simple reason why I do not routinely put them on my kilts. I make my kilts modeled much after the original tailored kilts, and none of these early kilts had belt loops. :-)