At the top of page 4 in the QS9000 manual you can read the following:
"The third party registration scope must include all products and services being supplied to one or more of the companies subscribing to this document, unless waived by the customer"
As I interpret this you can still be certified according to QS9000 but still not have to performe PPAP or other QS-steps to customers who do not want or require this steps. We have a approximately 5000 diffirent parts and we getting new parts every day varying in production size, from 50-100 000 000 parts/year. The majority of the customers do not want the QS9000 requirements.
Our certifications body says that we have to perfome PPAP for every part entering the building regardless if the customers wants it or not.
Can anybody help me out here???

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The requirements for PPAP is in Para 4.2.4 of the QSR.
The companies subscribing to QS 9000 for which PPAP is required are DC,Ford,GM and those listed on page 79 of the QSR.
If you have one of these companies for a customer then you are not required to have PPAP data for your other customers.
If you do not have one of these companies for a customer then you are required to do a PPAP for all of your customers, in which case you probably should not have registered to QS9000.
I may have muddied the waters but it is food for thought