Whilst this depends on the actual PDF being used, as a general rule: yes. On one hand, a blank page/template in GoodNotes is very small, only taking about 8 KB. By contrast, a PDF template will typically be larger than 8 KB. As such, if the PDF that you use as a template is larger than around 8 KB, the individual pages with the PDF template will take up more storage space.
Whilst this may not be hugely relevant for smaller notebooks, the use of custom PDFs for larger notebooks can result in substantially higher storage space usage (in addition to more space needed on your back-up applications).