I believe they were removed due to the bugs associated with them, of people paying money for one, but never getting a box, because there wasn't anything to fill it with. So, instead of having to constantly refund people, they just removed them.

The boxes work by filling them with stuff that didn't sell before being rotated out, from the shops, if all the weaponry boxes, for example, were bought before more weapons could be rotated out of the shop, no stock would be left to fill a weaponry box, so you'd buy a box, but not get a box.

Posted by: @dragonus

What happened to them? These no longer seem to be available.

Weaponry Box	24t
Jewelry Box	24t
Protective Garments Box	24t
Clothing Box	24t

I could have sworn I posted about this at the time, but I'm not seeing it now, so I must not have. But yes, ArchMagi is correct. They were causing a number of bugs and other issues, so they've been removed for now.