There is a bit more public information on the narco sub found in Ecuador.
Special to the Chronicle
“Experts have studied the narco submarine, which sits in Guayaquil, Ecuador. Painted a camouflage pattern of blue, black and gray, it is believed to be able to submerge about 50 feet.”
Details are still sketchy. I want to know if they had any ESM equipment, and if so, how sophisticated?
I’m really surprised that the smugglers chose an “Albacore” hull form that is optimized for performance under water. Surely it would spend most of its time on the surface and submerge only when it recognized there was a search unit in the area. A shape more like a WWII submarine would have made more sense in terms of covering long distances on the surface. And why the rudder above the hull, but none below? I’m impressed that they could build this in the jungle. I’m less impressed with their design choices, so I suspect the designers may not have been as expert as the DEA seems to think.
There is the possibility they intended to snorkel all the way? In that case the hull form would make more sense. Concern for snagging the rudder in the jungle where it was built might explain the rudder.
Chuck Hill's CG Blog 
The more I think about this, the more I want to eat my words. Wood and fiberglass construction would make the sub naturally stealthy against radar. Small size would make it stealthy against active sonar, especially if they turned toward the source. If it recognized that there was a passive acoustic sensor in the area, going on battery would make it very hard to detect.
If the concept of operation was transiting on snorkel, there is a good chance it would be accompanied by one or two surface vessel, probably fishing vessels, that could maintain a lookout and warn it when it needed to fully submerge and go quiet. I would think one close by and one about 10 miles ahead. There might be an all clear signal too. A fishing vessel close by, would tend to mask the noise of the snorkeling submarine.
(The narco trafficker who claimed to have invented the towed unmanned container that submerged hydro-dynamically described using three boats working together. )
I have a more sinister theory for the rudder being only on top. Being that the conditions in the sub are miserable, I think the drug traffickers know that if the crew can only steer the vessel underwater they’ll be more inclined to spend more of their time underwater instead of taking breaks on the surface where they can get fresh air but be detected.
Check out this sight for background information:
http://covertshores.blogspot.com/2010/06/narco-submarines-torpedoes-and-semi.html
Thanks!
A bit more information here: http://www.npr.org/2011/04/20/135574444/ecuador-seizes-drug-running-super-sub