Zukofsky's dead.
In the old timeline, yes. But CASINO ROYALE negated everything that happened beforehand, moving everything to a separate timeline. That's the point of a reboot. So if Valentin Zukovasky exists, he is alive.
That said, I doubt EON will bring him back. Zukovsky was born out of the GOLDENEYE script, and I think he was handled very well. GOLDENEYE was the first Bond film to be made after the fall of the Soviet Union, and really addressed Bond's place in a world without the Cold War - the underlying theme is that while Bond needs the world, does the world necessarily need Bond? Zukovsky really reflected this: he was an ex-KGB agent who turned into a gangster with the foundation of the Russian Federation and her economic troubles in the early 1990s. The end of the Cold War formed a significant turning point for many of the Russian characters; Valentin Zukovsky, Xenia Onatopp (yes, I know she's Georgian), Arkady Orumov and Boris Grishenko were all left behind by the new Russia. There was no longer a place for them, so they all kind of went their own way (or, in Boris' case, drifted aimlessly until Janus found him). Now that the Cold War is dead and gone, it would be very difficult to reimagine Zukovsky simply because he had to be firmly established in the Soviet Union. It's getting to the point where he would simply be too old to be reimagined; right now, the most EON could do is write him as a promising young KGB/GRU/SVR agent who was being fast-tracked for promotion in 1989, but was left to his own devices when the Cold War ended.