I've been asking the same questions.
The Brits are usually too good to get caught flatfooted like this, certainly not twice in a row.
Pueblo was taken when the nearest US units were almost an hour away by air, and absolutely no precautions had been taken beforehand, I can't imagine ships being inspected by boarding parties without anything smaller than a frigate standing by in visual range just in case. If nothing else, the inspected ship itself might have been an ambush setup.