Thieves guild doesn't count: unlike other guilds, they are not unified across Tamriel but every province has its own criminal syndicate.
anyway, Beth kills the guilds because they got tired of them and are likely changing to province-specific guilds.
In the next game....The DB is back,The Thieves guild got the eyes,The Blades have reclaimed their position as the emperors bodyguard.
Reclaimed? Blades THEMSELVES left the Empire because Medes were not Dragonborn

;
And since our Dragonborn is the last Dragonborn and they served the Emperor only because he was a Dragonborn, they will very likely never be Empire's Spy Force again... and very likely cease to exist altogether.
And I would argue that the Dark Brotherhood is also in a good shape. The hierarchy of the Nightmother is restored. The non-believers are dead. The Dark Brotherhood gaining a massive spike in their reputation because of
On other hand, they no longer have sanctuaries in Tamriel besides the Dawnstar one. And seeing how Sithis abandoned Morag Tong in an similar situation, I can see Beth killing of DB for good and introducing a new Assassin's Guild.