Tapping backhaul providers would do the same job more simply
Cables are cut by fishing boats all the time. They are pulled up onboard a ship and repaired all the time. So although repair and re-splicing is fiddly, it is also an everyday fiddly task. Not some impossibility as your article comes close to suggesting. If the 10KV was actually enough to damage a fishing trawler we'd be very happy -- sadly it readily dissipates in seawater. That gives NSA a simple technique to cut a live cable -- clamp chains to the cable 100m apart, chop the cable in the middle, pull up the chains.
The point Briscoe makes is that SCCN would know about this. But you can readily imagine some misdirection, such as cutting the cable once again a few Km away to give a despatched repair ship something to fix.
The question is -- is this likely? And it's not really, because of the backhaul problem. You've applied your splice, you've got a copy of all the data, now how do you get that data back to land? The only choice is to hire wavelengths or complete fibre on the same cable under some pretext (such as connecting Pine Gap back to the USA). That's not really possible to do mid-span without a high chance of stuff up (such as the wavelength used gaining power mid-span, or a FEC incompatibility).
The NSA's desire is much more simply met by tapping the backhaul fibre heading away from the landing site : there's no water, no voltage, no close monitoring, no forward error correction. Just simple dark fibre in a conduit.
The NSA could require a Room 641A type arrangement to tap each cable as it is patched from the undersea cable headend to the customer. But Briscoe is saying that isn't the case (although he explicitly did not call out the Australian landing sites in his denial). Briscoe might well be truthful -- you can only imagine that having had Room 641A revealed by a junior technician that the NSA would look to less apparent ways to do the task.
I don't think it's likely that the NSA are using CALEA or other interception requests for transmission networks. Those legislative mechanisms don't suit transmission networks at all.
BTW, carriers don't encrypt link traffic. It was thought that there was no need. It's fair to say that the various leaks from the NSA are changing that view. However encryption of high speed, high latency, high natural error links isn't as simple as you might hope. That means it's expensive and thus the engineering desire has to overcome the beancounting hardheads.