It's not very expensive not to populate the USB receptacle on the the PCB.
Sealing the hole in the case would be easy. You could have an removable insert in the case's injection mold so there's the option not to have the hole.
If they thought two case parts were too logistically complicated, or they already made the mold and don't want to mill it out to make space for the insert, they could insert plastic plugs with permanent snaps.
If they really didn't care, they could even just put they sticker over the hole in front of an unpopulated port.