AFAIK there is a way to communicate through radio with an underwater sub but involves complex antennas very long radio waves and complex signal processing, etc. There is no way a sub would be able to get a GPS signal under water.
It is possible to have a sub that runs under water most of the time and only occasionally pops up to get its location via GPS, but that would require very complex autopilot software, which the narco trafficers do not have yet.
Plus, subs are inefficient - the regular drug busts around here (central america) , when they find them, are regularly into several metric tons, usually on boats that are inspected while refuelling. That's just what gets caught... which has to be a very small fraction of what passes.
Google Narcosubs for more