A head Office should not be a sub-contractor, although I did come across one major multinational where many of the different functions- Purchasing, Transport/Distribution etc., were separate companies within the same group and could be thought of as sub-contractors.
Even if your supplier approval is carried out by your Head Office, it should still be audited as part of your certification. The question then is how to audit it.
It can be covered by a separate visit to the Head Office. This is fairly common for companies with several manufacturing sites and a Head Office which undertakes activities within the Standard. It will of course mean extra cost.
Alternatively it can be audited by making available the staff responsible for the process and all the records on your site, or sometimes remotely if effective communication links can be set up. You would need to plan and agree this with your Certification Body in advance.
What is not acceptable is to say it is not applicable as it is a Head Office function.
How did you do it in your previous audits?
Your pre-auditor therefore may be correct, although if no records at all were available, it should have been a Major and you would probably have picked up a couple more in the other clauses of this section.
Personally I think 15 non conformities in a pre-audit is good going and in fact helpful. It is much better to have them in pre-audit where you can deal with them in your own time frame than in your certification audit.