I doubt the police submits name only records to the FBI for not so serious offenses. Name submissions (without FP) to the FBI's NNCP come from multiple agencies, such as CBP or the IRS when your name comes up in an investigation regardless of if you committed a crime or not. It's possible that your name alone comes up with a hit on the NNCP without you ever having committed a crime.
The bottomline of my opinion is that FP is usually but not always part of "arrest". It does not matter to answer N400 form because the question
combined "arrested, cited, charged" into juts one question on N400. I think
during the interview, the IO should repeat that question but the IO may prefer brevity and only asked" Have you ever been arrested". If an applicant
was only cited but not arrest (taken into polcie station to do FPOP, mug shot etc), he should not just answer one word "NO" otherwise he may face beiong
accused of lying. If he answer No he better follow up with "I was cited".
In case of the OP I find he did not explain his situation well. Did he
answer "Yes" on N400 to the "Have you been arrested, cited, charged?"
If he did, then he could argue he never intend to lie because he alreayd dislosed
his incident on N400. If he answer No, then why did he still carry
those court documents? If he just answer NO on N400 form and brought
those court docuemnts just in case the IO knew his incident then he was in big
trouble for lying and he had no more good argument anymore.