I'm guessing it was just a coincidence between the 96 hour mark and when the capable ROVs finally arrived on site. They deployed the ROV that discovered the debris in the early AM today. Based on the fact that info was already leaking prior to the coast guard announcement, it was probably known for several hours before being made public.

Edit: Yeah, they probably had reasonable suspicion that the sub was gone. But until they had evidence, continuing search and rescue seems like the prudent thing to do.