I've been told that there is a desync in the guild finder and guilds that are in thieves dens. I can tell you it's not just thieves dens that guilds aren't showing in the guild finder. If you're not in a major base game city your guild will likely not show. Guilds in Alinor, Elswyer, Murkmire, Vivic and other dlc areas aren't showing in the finder.