The person doing a passport interview knows nothing about what might have caused the delay. They are just there to tick some boxes, nothing else.
I don't think Blackhole will every have problem again. Whatever they may have wanted to clarify has been done and dusted and passport issued. It took them 23 months, and eventually they are sure that Blackhole is not that "bad guy". I would think that even if someone by chance had couple of details matching with a terror suspect or a hardcore criminal, they would carry out extra checks. Somone might just studied at the same college as a suspect, or name was somewhat similar to a suspect, or by chance thier part of name and father's name matches with part of a suspect's and suspect's father's name etc.
It does not mean that an applicant had exact same name and dob as a suspect. A mere slight match with someone might have triggered extra checks by HO.
Now the passport number clearly distinguishes between the two, and it has been recorded that passport number 12345 holder is MR A the good guy, British Citizen, and not the bad guy who is a citizen of mogamboland who is on suspect list.
