Your question is wrapped up in a couple of assumptions about movie clips and GC behavior, and I think addressing them will answer your question:
when I destroy the container movieclip, will flash get rid of the event listeners inside of nested movieclip's custom class ?
You can't destroy class objects in AS3, including movieclips. The GC destroys them automatically, but only when there are no more external references to them. Simply removing a movie clip from the stage doesn't "destroy" it in any sense - the object is still there, it keeps all its event listeners, you can still rotate or scale it, or stop it or play it. It's still a normal MC in every sense, it just doesn't happen to be on the stage any more, so it keeps all its events and listeners like any other clip.
flash has a tendency of not killing listeners along with the movieclip itself once it is removed from the stage...
Flash never automatically removes listeners from anything, including movieclips. What you're thinking of is that Flash can garbage collect objects with listeners, and if an object gets GC'ed it will no longer broadcast events. However, the object will only get GCed when there are no more strong references to it, so if you want a movieclip to get destroyed despite having listeners, then you should use weak references when you listen for events, like this:
addEventListener( Events.BLAH, myListener, false, 0, true);
The final argument ("true") specifies weak listeners. But remember, using weak listeners only means that having listeners will not keep the object from being destroyed. In other words, the listener will not count as a reference, but you still have to remove all the other references besides listeners before the object will be GC'ed - simply removing the object from the stage won't cause it to be destroyed unless you have no other references to it.
But I got to know how flash handles moveiclips that are nested into a parent movieclip and has enter frame listeners.
It handles them exactly the same way regardless of whether or not they are nested. The only thing you need to be aware of is, when you add one MC as the child of another, they each keep a reference to each other, so neither one will be a candidate for immediate garbage collection as long as they have a parent-child relationship. If you remove the parent clip from the stage, and destroy all external references to both clips, then they will be candidates for GC, but not until a mark-sweep occurs. Google mark-sweep if you're not familiar with this kind of collection, and all should reasonably clear.
Hope that helps!