Can penalty for not declaring food items leads to future H1B Visa denials?

My H1B was picked in lottery on 11th April 2016 and in June 2016, I visited US for business meeting on my existing B1 Visa. At customs I was fined for not declaring Rice and Peenuts. Could this leads to Visa denial? My visa application is at case received status till now.

No, it doesn’t. You may be subject to baggage inspections b/c of this past history, but I don’t think they would deny the visa for this.