Hello,

I play United Empire. I had democracy with 3 strong political parties (military, science, production) each more than 20% in votes. The rest had all the game less than 5% of votes.

Average happines in the empire was around 90%

In spite of this, I encountered revolution, which put my empire into anarchy for few turns. Happines fell down to average 10%. In almost every star system was iminent danger of mutiny.
After that was my democracy changed to republic with almost 60% of religious senate.

Question is, if there is programmed some kind of "Al Kaida", or is this just an bug? Or something between?

Is there any possibility to haunt these terrorrists?

Unfortunately I already do not have save (I just played further and hoped I can swich establishment later and repair damage in my imperium)

I'm thinking that you went over the optimum number of colonies... this will bring down happiness in your Empire quickly, making some colonies revolt.

Be careful not to go more than one colony over the optimum.  If you do, make sure you get the extra colony techs with them, or you're headed for what you describe!