The fact that Ballard was surveying the wrecks of the Scorpion and the Thresher for the Navy, prior to actually searching for the Titanic has been known since the late 1980s. The story, at the time, was that the Navy wanted Ballard to use the ROVs to photograph the wreckage of both subs, to obtain higher resolution photos of the Thresher and the first real look at the Scorpion.

Thresher, lead boat of the class that was renamed after the second boat, Permit sank due to poor welds in a high-pressure salt water conduit — the welds failed during a test-depth dive, the reactor scrammed and the boat fell backward, until it imploded, falling in six major pieces. As a result, the Navy implemented the SUBSAFE program, which included X-Rays of all submarine welds.

Scorpion was lost more than 5 years later, off the Azores. Acoustic and seismic evidence pointed to an explosion near the surface, the damage indicated an internal explosion near the bow torpedo room and the fact that the boat was traveling in the 'wrong' direction indicates a possible torpedo malfunction. However, the official Navy finding is inconclusive — likely to hide the fact that the Scorpion was carrying torpedoes with known-defective batteries, that could catch fire, start running on their own and potentially explode. (Scorpion was also carrying at least two nuclear torpedoes.) The boat sank bow-first, very rapidly, until the rear compartment literally telescoped into the operations compartment amidship, ripping the vessel into two pieces.

Ballard has said, previously, that the Navy wanted him to find the Scorpion's nuclear torpedoes, and develop a plan to recover them. Officially, IIRC, he couldn't find them.

As for the reactor vessels — unlike most Soviet boats, US boats used very compact, very heavily constructed and very heavily shielded — they are designed to withstand pressures in excess of the deepest trenches in the oceans, far greater than the 1,500-1,800 feet that most modern U.S. subs can withstand. Furthermore, the scram system is designed to immediately close all reactor interfaces in the event of cooling system pressure loss, precisely due to fear that a downed U.S. sub would poison the U.S.'s prime fishing grounds.

Lastly, Ballard had found the probable location of Titanic prior to the "rediscovery" — he was just unable to effectively search the field, due to weather, funding and technical programs. When he returned, partially funded by the Navy, the first item they discovered, with less than a day left for their search, was a boiler. They followed the debris field, and finally came upon the bow.