With so much evidence pointing to the pilot who was/is Anwar's cousin one would think that Anwar was either in on this or knew about it and he would stay in the shadows and keep his mouth shut while the government tries to drag him in for questioning.
However look at what is happening --
Anwar comes out and accuses the government of incompetence in their response to the disappearance and the government is scared to death to point the fingers at his cousin Captain Shah as the likely culprit in the cockpit.
Go figure --
Pushing the speculation envelope, I would say this was mostly a spur-of-the-moment decision - a few days max. I haven't seen any evidence to the contrary. Then it's not likely at all that Anwar knew about it.
Also, isn't he under arrest already? And that is a very contentious situation in Malaysia. Seems to me he would want to use the event to further publicize his situation, not the reverse. The weaker the current gov't and PM are, the stronger his own position. And there's not a whole bunch more the current gov't can do to him. He's facing 5 years in in jail which comes with a permanent ban on holding political office so they are not able to intimidate him.