It's also true that Scribus sometimes chokes with long files period, although I think this may be only when there are many graphics. In any case, I have found that it works better for me to keep Scribus files under 50 pages or so, and to use a different file for each chapter. The page numbers can be set for each chapter in the document setup. The first page of each chapter usually needs a different master page from the rest of the text, with a different header and the page number in a different place. I find separate chapter files easier to work on in general, anyway.
(Also I start each chapter with a right-hand page and give it an even number of pages.)
After exporting each chapter to a PDF into a folder called pdf_assembly, I concatenate the PDFs with a PDF editor, I use PDF995. Print quality pdfs may be huge, and there is an advantage to keeping the chapter pdfs separate if you want to send them by email.