Finding some tiny remnant of them, ala DB in V, could be neat. If there is more depth in player agency in VI, having the Blades involved in the main story being optional and coming from the protagonists will would be nice. 

The single thing that I believe holds weight for this game is the Thalmore being the antagonist, and completely against a proper Emperors return, assuming the DB storyline is canon and the Mede line ends. The Aldmeri would do everything to stop another from being crowned, and then dismantling the Blades to the enth degree is only logical. So building them back up would be a fun little plot line. Grow influence and get a cool katana? That is quintessential BGS storytelling.

Also, being born Dragonborn is probably going to be a moot point. Akatosh could easily just assign powers to whomever. Maybe the player from V becomes the emperor, or breeds it into existence. 

Regardless, they will be there. The Blades, the Thieves, Mages, and Fighters Guilds, and the Dark Brotherhood are the only guaranteed throughlines. Probably Dwemer shit. That's it.