Coffee beans appear to be missing from Port Azoun's usual import seller. I don't know when this happened, but they certainly used to be available there and there was never any announcement indicating their removal, so I assume it's unintentional.
Given coffee beans were also removed from fishing crates (intentionally), there is no longer any way to acquire them outside of opening static barrels/crates (for a whopping one bean every thirty containers, perhaps) or paying a ludicrous amount of money to a very specific smuggler.