I've had some issues with the mods working and I've just discovered that if you click the game to play in Steam and just leave the launcher up for a bit, the mods will update. There's no progress bar or anything, so it's a bit confusing at first. You can notice it happening by starting the launcher and then immediately clicking Data Files. At first, all the mod names will just show up as the actual file names and there won't be any subscription status info. If you close that and wait and reopen it, you can see more info populating, and eventually newly subscribed to mods being added.