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?
There is no competitive difference between the female and male Wii Fit Trainers in the Smash games - the differences are purely aesthetic. Their Smash 4 and Ultimate Wiki pages list no differences - they would do so if there were differences. This also applies for the genders of Villager, Robin, Corrin, and Inkling, as well as the alternate costumes of Olimar/Alph and Bowser Jr/Koopalings.
Sakurai stated that any changes between characters that are more than aesthetic and reflect different attributes warrant a separate character slot e.g. echo fighters. No difference in attributes = no separate character slot. For example the only attribute differences between Peach and Daisy in Smash Ultimate are slightly different hurtboxes during certain animations.
EDIT: As per Toomai, it's not mechanically possible for different costumes to have different hit/hurtboxes. There is only one moveset file (which contains this data) per character. Lots of other stuff can be costume-specific, but not this.
