It really depends on your content structure: the more nested the better.
Kirby is quite mighty and can handle more than you might think. There are many sites with thousands of pages out there performing like a charme. But as you mentioned, being based on a filesystem has implications, so its much easier for Kirby to handle a content structure where thousand pages are nested, so that each page only has a couple of subpages - compared to one where all thousand pages are subpages of a single parent page.
However, even in these situations, caching can go a long way to achieve great performance.