You also have to consider that the US at least would be strongly inclined to bomb that kind of thing out of existence... it would after all be a huge potential threat if used for something other than smuggling drugs. We're not trying to fight the cartel subs like we would an invading military, and if we did, they'd have no chance. The payoff stops being worth it when fucking up means you lose the sub and the cargo without warning.
The US Navy is already involved a fair amount, as the article described the torpedoes getting detected by their acoustical signatures. That is not US Coast Guard-built skills, equipment, and expertise, so I wouldn't be surprised if it turns out the military is involved way more than we are let on.
This presents an interesting operational challenge for the US Navy. Say they are authorized to engage and terminate without warning any submarine operating within US territorial waters that is not a registered civilian submarine broadcasting its presence, or another US military submarine. Just how would US naval underwater assets know who each other are without compromising their mission if it involves staying undetected? The closest approximation I can think of is encrypted sub ID and anticipated operating theater within the next 24 hours, using a Gertrude-like system or some other two-way submarine communication (and there aren't any good current choices for systems in that field).
