The cat and mouse between these guys and the naval/Coast Guard units of the involved nations might in the far future see the introduction of full-blown diesel-electric, liquefied oxygen-bearing, water-cooled exhaust submersibles. Battery-powered and make the legs of the run only at night. Diesel plant is fed stored oxygen, gas expansion powers compressor-free air conditioning. Metal-oxide-based CO2 scrubber is regenerated from diesel generator heat while engine is run during day-time to recharge, as the smugglers stop and snorkel stationary to avoid wake-detection. Noise-isolating mounts reduce detectable range of running diesel generator. At or near the destination port, a disguised tender trans-loads the shipment, and resupplies diesel/food/reverse-shipment-goods. Between those technologies and operational discipline, it would be a big PITA to detect.
It's a good thing these future submarines would be immensely more expensive, and narcos are not known as good employers guaranteeing solid operational secrecy, as such an unusual setup would bound to get disgruntled/prideful operatives blabbing/boasting. By the time they get around to it, involved nations will probably litter the nearby ocean floors with a SOSUS-style dragnet, and that will likely put this smuggling route out of reach of all but nation-state-grade narco-cartels willing to spend about multiple billions in R&D and $1B US per construction unit to upgrade to military-grade diesel-electric submarines with their more advanced acoustic signature mitigation systems and protocols.
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).
There's additional (comparatively) low-cost actions that can be taken to avoid intercept such as:
Make it autonomous (to avoid the cost and complexity of air conditioning and crew oxygen).
Use an ADS-B/Mode-C receiver, FLIR camera, and AIS receiver to detect any nearby aircraft or vessels. If there's something nearby, dive.
Monitor VHF and UHF airbands (and frequencies used by military tactical voice/data systems), and if there's any strongish signals there, assume that's a nearby aircraft, and dive. You don't need to know what is being transmitted -- just presence is enough.
An uncrewed system means that endurance can be made very long -- so it's feasible to dive and stay down (with every noise-generating system shut down) indefinitely, multiple times, as evasive action. This application is latency insensitive -- as long as you can be assured that the cargo is still proceeding nominally, everything is fine.
It's a good thing these future submarines would be immensely more expensive, and narcos are not known as good employers guaranteeing solid operational secrecy, as such an unusual setup would bound to get disgruntled/prideful operatives blabbing/boasting. By the time they get around to it, involved nations will probably litter the nearby ocean floors with a SOSUS-style dragnet, and that will likely put this smuggling route out of reach of all but nation-state-grade narco-cartels willing to spend about multiple billions in R&D and $1B US per construction unit to upgrade to military-grade diesel-electric submarines with their more advanced acoustic signature mitigation systems and protocols.