I know this is pedantic, but that's exactly what I would expect from a security clearance vetting process.
If the FBI investigates a spy seen driving a silver Honda Civic with license plate ABC-1234, and looks into an unrelated civilian who drives a silver Honda Civic with license plate ADC-1234 in case their witness misremembered the license place, that doesn't mean the unrelated civilian was "investigated by the FBI".
I'd say determining that is exactly the point of an investigation. That fact that it ended well doesn't change the fact that the process happened, and was triggered by said person.
In this specific case, the security officer made the correct decision in having him leave out this detail from the clearance form. Makes for a good story, though.
To me, these are the same, so I guess that's probably just my layman's view then.
After they found and identified who created it, the investigation was dropped before they investigated any particular person.
'course, with the general urge to be "tough on crime" and the inevitable occasional horror-story of truly heinous behavior discovered many decades later there probably isn't a lot of political will to support reasonable statutes of limitations, so I wouldn't be surprised if some of this stuff never expires.
Edit: it's a story from 1988, so at the time it was only 45 years ago.
I don't think it's entirely unreasonable for a special vetting process to have stricter standards.