The only gems unlocked by the hotfix are the one that are awarded for the future (at the time of the hotfix) invading factions: naga and pirates. Because those were the only ones timegated by design.
The rest are presumed to be immediately available as “anytime” quest rewards and routinely available boss loot.
Here’s the relevant quote from the hotfix announcement:
The stones you expected to see on the vendor (but didn’t find) are the ones described in the first paragraph.
The hotfix wasn’t designed with the bugged Shuddering Hollow boss in mind.