I am hoping adequate research is underway for larger underwater launch systems of un-manned fighter aircraft, camera drones and even bombers that are launched from submersible carriers.
Give the boat stealth from the minute it leaves home port.
Not quite what you’re looking for, but there’s plenty of pretty out-there stuff in the unclassified DARPA budget, including development of high-speed supercavitating transport submarines. “Programmable Matter” (Think the T-1000 Liquid Metal Terminator) is another good one.
http://www.darpa.mil/Docs/2010PBDARPAMay2009.pdf