User blog comment:IamJakuhoRaikoben/Chapter 439: Albareth Empire, Review./@comment-5969537-20150610014537/@comment-4829046-20150610141433

Then again, not all the Dark Guilds that were fought in Ishgar have been disbanded. I doubt they count though, since I think Makarov would know the number through some Council Registry and Council probably won't include rogue guilds in that. Also, remember how big Phantom Lord(not a Dark guild but...) was? I'm sure the Phantom Lord section was devised waaaaay before thinking about this 'total number' thing but while Phantom Lord was one guild, they were running various Guild buildings throughout the country and maybe other guilds are also operating in such a way after all this timeskip. In which case, the number is appropriate. Also, he said 'guilds' not 'mage guilds' right? Maybe Treasure Hunters count? I sincerely hope not, but Mashima implied that there was a whole bunch of Treasure Hunter Guilds in Ishgar.

Overall, not much point thinking how the number is made up. There are a multitude of possibilities. Maybe the other Kingdom is so strict that its military tactics are echoed in all the guilds and any guild that attempts to go rogue is immediately crushed unlike the less strict Ishgar. In which case, they would just be collective 'guilds' rather than legit or dark.