Well, I know that the region in general has a real problem with piracy and that includes even some large merchant vessels being assaulted so I presume they operate in the Java Sea also.
But since you mention it now I have myself another littlle research project to do.
A few days ago coincidentally I was reading some about the Battle of the Java Sea and it was commented on about the stripping of gear from the Houston and the Perth.
The Houston and Perth (has its wreck ever been found?) are in the Sunda Strait and if they have been stripped I would dare say it was by divers looking for souvenirs and the like rather than pirates. I had a look and you are right there are pirates in the Malacca Strait but I would guess a fair few hundred miles north of where this plane has gone down.