They were. Disney fukked that up when they bought the franchise. In the early 90s he didn't consider the books canon cuz they were looked at as fan fiction and there was no order to them. The popularity of the Thrawn trilogy changed that, and Lucas got on board with the EU, and games, and books were considered canon, with his approval with the exception of the comics. They were their own world.
That creates an issue with what is considered canon and what isn't now. Darth Maul surviving was in the comics which weren't canon, but was a plot in the Clone Wars which is canon. Also Darth Bane was part of the EU that got scrapped, but was also in the Clone Wars.
Lucas pushed for Revan to be in the same episode, but the director scrapped him at the last second . If that's the case, then that opens the door for previous characters and events to become canon again with the obvious exception of Luke's wife and son, the Solo kids, and the Yuuzhan Vong. They even said they may draw on the EU for future projects including the movies. IMO I think they did that with Rey and Kylo Ren. There's a lot of speculation that Ren= Jacen, and Rey=Jaina which makes sense if you think about it.