In both the case of the USS Thresher and USS Scorpion, the subs were lost because the emergency system used to blow ballast wasn't up to the task of diving to those depths. There was freezing in the system due to the extreme pressures they were working under.
Sub Brief on Youtube has good analysis of the loss of both boats, going into the details of the likely reasons they were lost.
The possibility cannot be denied that Rickover might have tried to downplay the safety risks of having a single nuclear reactor on a submarine as the sole means of propulsion. Soviets often would use two reactors on their early nuclear boats for this reason alone, and on some of their single-reactor designs, they would either use backup electric motors or they would use highly reactive metals to produce gas to blow out the ballast. Of course, Soviets were often trading off noise for deep diving and survivability as a result.
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