Well, to begin with, Operation Unthinkable did not factor in atomic weapons as it was a British plan made prior to Trinity with extremely limited knowledge on the progress of the Manhattan Project. This means that the use of atomic weapons, coming as it would several months, would be an ad-hoc effort. It's debatable whether there would even be any use of the bomb, given that the political scandal caused by an essentially unprovoked attack on a major ally could interfere with the attempt. Early atomic bombs were too unwieldy to be utilized tactically, so any nuclear raid would be a strategic bombing one. Given the extensive intelligence penetration of the Anglo-American governments in general and their nuclear programs in particular, the Soviets would have good odds at knowing when, where, and in what strength a atomic strike force would be going, giving them the capacity to mount intercept attempts. The main interceptors would be the Yak-9PD along with a smaller number of La-7TKs, as these models were built for high-altitude interception. Whether they'd succeed is of some debate and is ultimately dependent on a number of factors, some of which are unknowable. On the whole, though, the limited number of nuclear bombs means their not likely to make much of a difference in the early stages of a Unthinkable-style war. Their importance will grow if the war drags on for an extended period of time, but I'm dubious the WAllies have the will for a long war with the Soviets given the political context in which Unthinkable would be executed.