Because it's fantasy made up by random people. And a lot of it conflicts with the actual canon stuff, it makes sense to de canonize it otherwise they'd have to sift through every EU thing made ever to make their movie make sense, and have it adhere to some of the ridiculous powers and figures that the EU has introduced.
It's fantasy made by people who have been licensed to do that. The likes of BioWare for example paid money to LucasArts to make the game in Star Wars universe. Even worse, they have decanonized stuff which they have made themselves (like The Force Unleashed).
In many cases LucasArts has intervened, for example the original plan on Thrawn Trilogy was that the rogue Jedi to be a clone of Obi Wan but Lucas said no, so Zahn had to change that and to make a new Jedi for that. In other cases, like Darth Plagueis novel Lucas himself worked with the author on the book. The Darth Bane trilogy basement was made by Lucas too. It's not that anyone could have write Star Wars stuff, but there were a selected few wgo got licenses to do that.
The shame is that pre Thrawn Trilogy things are very good and they don't contradict each other. After that trilogy things went bad and it was like a crazy race between different authors who'll make the Star Wars characters more powerful than Goku on DragonBallZ (and to be fair, some achieved that, as crazy as it sounds). That part was a no brainer that had to be removed, especially considering that it is anyway shit and it's on the same time as the new movies.
But stories of Naga Sadow, Exar Kun, The Old Republic stories, Darth Bane, Darth Plagueis, Kenobi novel, The Thrawn Trilogy had no need to be changed.
Anyway, I think that it won't have any effect at all. Movies anyway wouldn't have been affected from these stories, and most of the fans will have those stories anyway as their personal canon. There might be a nerd backslash if they without any particular reason decide to change stories from the past though. And if they somehow manage to change the names of Lucas/Leia kids, I guess that people won't be happy. And they too, because less people happy, less money for them.