Unknown but not Jian-Yang
It's not revealed who (if anyone) has taken the thumb drive. I think the missing thumb drive is just meant to show that Richard still is not entirely in control, and there still is some danger than someone else may release the Pied Piper AI on the world.
However it's very unlikely to be taken by Jian-Yang. Jian-Yang is impersonating Erlich Bachman and looks like he has taken all his money.
We can see this from the conversation between Richard, Monica and Jian-Yang at the party:
Jian-Yang: Richard, congratulations. It's your very close friend Jian-Yang, and I would like you to give me free shares of Pied Piper.
Richard: Okay, Jian-Yang. Uh well, you had plenty of opportunity to invest.
Monica: Still do. Yeah, you can buy Pipercoin.
Jian-Yang: Monica, two men are talking business. You can find your broom and fly away.
Monica: Suit yourself. I just checked the ledger, and the coin we issued to Erlich was just sold for $20 million.
Jian-Yang: Richard, is the mean lady right? Errich is now fat and rich?
Richard: Uh, yeah, I guess.
Jian-Yang: Where is he?
Richard: I don't know. Tibet still, maybe.
Jian-Yang immediately walks off and discards his Pied Piper hat on the floor.
Then at the end of the episode, when the documentary crew try to reach Erlich:
Interviewer: Are you Erlich Bachman?
Jian-Yang: Yes. I'm Errich Bachman. I can show you ID. That's my face.
I was a-fat, but now, I'm a-not fat.
The implication of this scene is that Jian-Yang is rich off Erlich's $20 million, not somehow off the thumb-drive.
Will there be more seasons about the missing drive?
S06E07 Exit Event was advertised as the Series Finale, and much took place as a documentary 10 years into the future. It seems likely that there will be no more episodes.