How do you know that they won't get at least something more meaningful out of this? Spain especially is very dependent on good relations with South-American countries, since Spain has a kind of diplomatic "gateway to South-America" role within the EU.
Bolivia lost all diplomatic credibility with Spain before this plane landing incident.
The Bolivian government unilaterally nationalised subsidiaries of Spanish private companies without any explanation, in exchange for nothing. I really doubt Bolivia will get the apology they believe they deserve at the EU level.
Well, if I become aware of them doing so, then I'll up my confidence in this method being more productive. But I can't, at least off hand, think of a time when this sort of approach has worked for a country that hasn't had fairly significant leverage.