FBI name check does finds it. It may delay your N400 process with FBI (during this time, it sits with the NBC).
As the lookout notice is concerned for only Indian Penal Code(You're told by the CBP officer as per your post), it eventually doesnt impact for you US Citizenship. But there will be some prolonged concerns, delays due to this.
Given your circumstance, working with a lawyer would help you.
Consult a lawyer before filing (May be for an hour or two).
If you get any RFE(Queries etc) during the process, you may again review it with the Lawyer.
Also take the lawyer to the N400 interview.
If I am you, I do dare to spend money for filing and a year+ wait time for my citizenship