"Two of his top national security officials at that time — his national security adviser, John Bolton, and the acting defense secretary, Patrick M. Shanahan — declined to comment for this article."
If he leaked intel of the operation, he plausibly would decline to comment on the article. That said, Bolton doesn't seem like the type to leak information about a Navy SEALs ops.
The article says it was in 'Early 2019' and he was NSA until September, so he was surely at the helm. But it also says Trump greenlit the mission, so I'm not sure how an advisor would be implicated in anything - unless your point is that the current admin thinks he might be the source for this story?
“The rumors are that the Navy's newest nuclear sub, the USS Jimmy Carter, has been designed for spywork, with a "special capability... to tap undersea cables and eavesdrop on the communications passing through them," according to the AP.”
ST6 is under the command of SOCOM, they do have the directorate to do clandestine work. To the degree that this article reflects any reality, it's also plausible that a partner in SOCOM (TFO/ISA) or an agency would be along for the ride to do anything specialized.
Lately, Trump has denied any knowledge of it. I bet since the FBI raid, Bolton himself isn’t contacting media very often. I bet confirmation of this story wasn’t forthcoming until it benefitted the case(s) against Bolton. And I bet that confirmation was very anonymous and very official.
