"Orphan files" means files left on the server that are no longer needed.
You may not have any unused files in your site files in Fusion... but you could have files left over from much earlier in the history of your site.
Looks like you've been working on the site since at least Fusion 8 times... several years ago.
With stacked pages for your catalog, every item has its own html page.
If you have 3,000 items, you'll have 3,000 pages just for those items.
You've outgrown stacked pages and need to consider going to a database solution.
BTW: if you just bought 11 in the past few days, you're entitled to a free upgrade to 12. It was just released late last week.