though AFAIK the terrorism charges for those indicted along with Yarkas were disputed only from outside the judicial branch

(And that includes Barkazanli as well as Alouni.)

As for critics outside the judicial branch, even the conviction of the main suspect was criticised for the use of circumstancial evidence:

Spain's 9/11 trial called 'a failure' | csmonitor.com

[El Mundo] said one problem was that the court's argument regarding Yarkas' role in September 11 rested on 'two weak pieces of circumstantial evidence.' One was that his number was found in the phonebook of a person who had lived with Mohammed Atta, the plot leader. The other was a tapped phone conversation that Yarkas allegedly had in which another person talks of entering 'the aviation business.'

To consider this a reference to September 11 was 'a flight of fantasy for anyone with common sense, and raises immense doubts about the seriousness of the verdict,' El Mundo said.