10,000+ nodes vs. 1 node with 10,000+ field collection items
Loading 1 node with like 10,000+ field collection items sounds like performance suicide if you don't limit the amount of items being loaded and displayed initially. And having to open a node with 10,000+ field collection items only to maybe add or edit one item will be really big pain then.

With nodes, much likely you'll never display all of them at once. You very likely will have them organised in Views. Limited display, pagers, filters, lots of caching possibilities. When you want to add a node, you'll have a fresh node form, loaded in milliseconds. Plus you will have a much larger number of contrib modules available dealing with sortability, searchability, orderability and a lot of other -abilities that come in handy when organising content. Also when it comes to content import.

Go for 10,000+ or even 1,000,000+ nodes. That's what Drupal is made for.