One thing I`ve just noticed is that although the Deep Dwellers have supposedly dissapeared... they kind of appear. They were supposed to be sent into oblivion, out of existance... and yet they make several appearances.

How? As ghosts. There are several ghosts to be found at dwemer ruins. You can even talk to one in the Tribunal main quest. For some funny reason your character is too dum dum to ask any questions from that ghost and others seem to just ignore any attempts at conversation.

So how are these entities still here and not erased from Nirn? Were only the living dwemer banished from Nirn? If so, how would you explain that the dwemer ruin in Tribunal had dust piles but there were still plenty ghosts to be found there?

Also Skyrim is coming in 11.11.11 and I hear dwemer ruins are confirmed. Think we`ll see more dwemer ghosts?

The Imperial Library has some decent info on the Dwemer disappearance, including some theories, here:

http://www.imperial-library.info/content/definitive-guide-dwemer#6

Some ideas I recall reading before that explain why Yagrum and the Dwarven Specters are still around include the disappearance only affecting living Dwemer in the world at the time. (Yagrum was in the "Outer Realms" at the time and was unaffected while the specters were possibly dead beforehand.)

There are tons of theories and ideas floating around.