I couldn't find any posts about this, so forgive me if this has been addressed.
Almost every night, usually sometime between probably 1 am and 3 am Subeta time (I'm in PST so from like 10-midnight), every NPC shop will be empty and say, "Sorry, there are no items stocked." As I said, this happens almost every night and lasts for an undetermined amount of time. Tonight, some shops restocked a few items within ten minutes, while others remain empty. I'm sorry I don't have more specific data on which shops/when/for how long, but it is absolutely a pattern I've noticed.
I don't know if this is intentional or if other people experience it, but I just wanted to put it out there! I basically don't do quests during this time because I know I'll have to pay inflated user shop prices for some items instead of just buying them from NPC shops.
[edit] Another detail I forgot to mention: Even when shops do begin restocking again, there are often only five or so items—much fewer than would be there in a normal restock.
I've been wondering about that too! But it's been nice, the whole "you have to wait 5 seconds between purchases" thing doesn't seem to be an issue when the stores are down.
They are stocked but, like you say, it's minimal.