Well that is not entirely true.
Dr. Ballard's main goal was to find the Titanic, but he needed a lot of funds, and the US Navy agreed to fund it, when he requested funding from them, but with the condition that Ballard first would go out and locate the sunken U.S. Navy submarines Thresher and Scorpion for them.
Once he found and photographed them, Ballard went on to the 'main quest', so to speak.
So the actual mission for Robert Ballard and Jean-Louis Michel and their team was finding the Titanic. Locating these subs was a priority for the Navy, not for Ballard, but he could not have done it without the Navy's backing and funding. You make it sound like he accidentally came across it whilst on another mission, this is not the case, nor is there a cover up, really.
I'm not keen on people still going down there for tourist visits and taking bits off of the wreck and so on, to be honest though.
Regards,
Fred