that sentence is a contradiction in itself...
if you size-mod a character, the hitboxes will adapt to it's new size, meaning that they will act different from a default costume, when playing online or reading replays, the game reads inputs, so if you take the modded costume away, the replay has certain inputs, that wouldn't work with a normal costume, and thus it desyncs, same on wifi, only that it's right away, because the other player's game is reading your input while it doesn't know that your character is a different size.
now, if you mean it'll mess up the hitboxes, as in, they'll be all over the place, then nah, it shouldn't happen as long as you leave the bone indexes untouched.
Doesn't happen when you make the character twice as big, and I'm talking oneslot size mods, as in using the EyeYellowM bone. If does effect the hitboxes, then why didn't my SMU Bowser work? Made him twice as big (was an old hack) and his hitbox was nowhere near his actual hands and etc, so I decided to just make him over Giga Bowser...
Don't do bone mods. Some bones are used for more than one thing. More often than not, bone mods of some characters tend to mess with certain bones they shouldn't which can cause glitches with not only the camera(One of the RotNs are used for camera stuff), but collision detection as well(Yes the game uses specific bones for that and messing with those or their parents is never a good idea).
I remember deleting a certain very popular size mod of D3 long ago because his collision detection was bugging out with that skin, causing warping and sudden SDs from said warping.
I've done my fair share of size mods, bone mods and porting a few characters over each other (Mario Bros over Ice Climbers) to know what bones to either not touch at all, or only mess with in a full moveset change, as in all costumes use the new bone position/order and the FitCharacter.pac also uses it (like changed bone indexes)
For Child Malon, all I planned on doing with bone edits was renaming her HairAN bone and making it bigger and moving it so the other hair bones was in better position for her rigged hair. Didn't even change the bone indexes.