Hi Atapia,
I looked into this one and understand the issue you are facing. I am afraid there isn't any way to not show Product bundle if it is added in the quoteproduct. This is because product bundle itself is a record which is associated to the quote and when you try to search for products, it will show all related records, including the bundle. In word template, there is not way to filter the spcefic records, it will show you all record.
You can have some kind of restriction on quote product entity such that users wn't be able to add the bundle product (if that suits your requirement)
Hope this helps