Why are the thugs not listed a minions? Are they not organized enough so they're not a cohesive unit? Did they just not want to teach that rule yet? Now that I know the rule should I treat them as such next time I run the beginner adventure? If I use them in later adventures should they then be treated like minions?

Most likely they aren't a group of minions because each is supposed to be dealt with individually since they provide one Gamorrean per player.

I think that its because the story introduces notions of the game one by one. The notion of minions only appears and is explained when the 2 squads of stormtroopers arrive.

Its like initiative. For the Gamorean encounter players and non players characters didnt have to roll for determining initiative. Initiative is explained a few chapters after the cantina's introduction.

Thats the spirit of the whole story : to discover step by step the mecanisms of the game.