Good morning Frink,
I always write my approval programs to allow for alternate means of approval for contractors/suppliers who don't 'fit the mold.' Typically I will review a chunk of risks (do they enter premises, do they impact food safety, do they impact business continuity) and get together items that you would need to have them go through for approval (insurance, licensing, possibly GMP training if they enter into GMP areas). I then have the other 2 members of my approval team review and sign off on (I do miss things on occasion).
Sending a one size fits all questionnaire to contractors that it has almost no common ground with always seems a bit cheesy to me and weakens the intent of the program (risk based). I guess you could do it and explain to them that putting N/A is ok in areas that are N/A.