I had the same issue, an odd bug that Paradox will hopefully soon get around fixing. Here you go.
As a band-aid solution for people who can't make Workshop exclusive mods work, follow these instructions:
1. Subscribe to the mod you want in the Workshop. Steam client will begin a download of EU4 Workshop Content.
2. Once the download is completed, go to .../Steam/userdata/[user_id_number]/ugc/referenced/[18-digit_mod_id_number]/mod. It will contain the .zip archive of the mod. If there are multiple 18-digit folders, look around for the one that contains the mod you want.
3. Copy the archive to your mod folder (the one in Documents).
4. From the archive, extract only the file descriptor.mod and place it in the same folder.
5. Rename descriptor.mod to match the name of the mod's .zip archive (e.g., if you have better_ti.zip, rename descriptor.mod to better_ti.mod).
6. Start the game - the mod should be listed in the launcher, activate it there (or, if you're using Mac or Linux, in Steam right-click EU4, go to Properties -> Set Launch Options and add: '-mod=mod/[name].mod').
If you have trouble opening the .zip or extracting descriptor.mod, try using a different archiver - 7-Zip should do the trick. (Winrar does not work in this since steam workshop mods have been packed in some odd manner, 7-Zip works though)