after omnitron is destroyed...

Do you still play cards from the villain deck?

I'm not entirely sure, If he is destroyed, but there are still devices in play, I would assume yes because his rules state to remove his character card, but doesn't say anything about playing his deck. Since the game is still going on you would still play a card, you just wouldn't recycle cards from the trash or play an additional card anymore. That's how I interpret the rules anyway.

Here's what I've got in my Clarifications doc in this subject, taken from an official ruling from the designers:

Playing cards after reaching 0 hp
 
When Omnitron is reduced to 0 or fewer HP, the Villain Character Cards are gone, but the Villain Deck is still in play. The rules say that on the Villain Turn, regardless of which Villain you’re fighting, you play the top card of the Villain Deck. Now, Omnitron can play a second card each turn, or pull a Drone or Component from its Trash into play, depending on what side of the Villain Character Cards is up. However, if there IS no Villain Character Card, those effects do not happen. But there is nothing to stop the top card of the Villain Deck from being played each Villain Turn.
 
Any card that has a line mentioning Omnitron at this point would basically have that line ignored, such as “restore X HP to Omnitron” or “Omnitron deals target X damage.”
 
So, in short, when Omnitron itself leaves play, the Villain Deck continues to produce a card each turn, until there are no Devices in play. Omnitron’s programming is in all of its robotic creations.

Thanks! Forgot I read that in your document!.

Spiff is, as usual, 100% correct here.