There is only one problem with allowing the covering of faces, identification for legal issues. It's REALLY hard to identify a person suspected of a crime when they wear a mask.
The remainder of the clothing could also be an issue, just as it is with the Amish. Long, loose, baggy, clothing makes shoplifting easier. When I was at Cabela's we would get buss loads of Amish come to the store. They had to be watched, REALLY, watched, they were famous for shoplifting. No reason to believe that a Muslim woman, or man, would not try to take advantage of the same. Also makes it easy to conceal weapons, legal or illegal.
Just other sides to the coin.