26 mile long Sector Patrol craft, hero detonates an atomic/nuclear device in ship's armoury, ship hiccups and requests "Please don't do that again."
The hero works for a shadow government employed to adjust other out-of-control governments.
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I think you might be mis-remembering Use of Weapons by Iain M. Banks.
"The ship was over eighty kilometers long and it was called Size Isn’t Everything."
Protagonist works for shadow government that stops out of control governments - check
Scene in armoury - check (see below)
Something flickered in the traveltube, and a capsule was suddenly there, door rolling open. “What’s this . . . trapdoor coverage, anyway?” he asked the machine.
“General Systems Vehicle internal explosion protection,” the drone explained, letting the humans board the capsule first. “Snaps anything significantly more powerful than a fart straight into hyperspace — blast, radiation; the lot.”
“Shit,” he said, disgusted. “You mean you can let nukes off in these fuckers and they don’t even notice?”
The drone wobbled. “They notice; probably nobody else does.”