I've noticed that at random times, all shops seem to clear out save for a 1 or 2 items. I highly doubt someone is buying them all, as that would take far longer than the time it takes me to buy one item. So is it a wipe to prevent items accumulating? Or something else?

Yeah it's a (sometimes annoying) automatic thing to prevent that too many items stay in the Main Shops, it's definitely not an error on your side or a bug. c:

Ah, yeah, figured it might be something like that. Quite annoying right now as I was using it to buy some trading cards. Oh well. It'll stock up again. Thanks for answering. (This can be locked then.)