In Smash 4, according to a friend who liked to play them, both female Wii Fit Trainer's model and hurtbox were smaller than her male counterpart's. This made it clearly advantageous to play the female version of the character.
However, the models look far closer in size in Ultimate. I haven't seen anyone at the professional level playing male Wii Fit (though I've seen several female Wii Fit's), but this may just be preference. Is there still a difference in their hurtboxes?