Such an arsenal of autonomous vehicles would have to survive for a long time - perhaps years - at the bottom of the ocean in cold, corrosive seawater unfriendly to metal and electronics. Communications will also be a challenge, because only very low frequency radio waves can penetrate ocean depths. The wavelengths are so long that the amount of data that can be transmitted is limited, so any complicated communications - beyond the "float to the surface" signal would probably have to be transmitted from a done at or near the surface.
On the other hand, Lockheed Martin designed an unmanned vehicle called the LMSW Cormorant that does something similar to what DARPA is asking for. So it's certainly possible, though nobody has flown anything like it yet.
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The non-technological questions include just how many seaborne drones would be needed and in what circumstances would they be called to duty. A strategist from 1998 might have predicted that drones would be needed in the Adriatic, near the Balkans. In 2008, the answer might be in the Persian Gulf, or perhaps the Taiwan Straits, or in the Sea of Japan near North Korea.