> still constantly run into things we cannot name yet.

Humanity has the opposite problem - we invent names for things that don't exist. We have no idea what dark matter is, but we have a name handy just in case. Same with gods, elves, dragons, aliens, etc.

I can't find one example of people not being able to name something that exist. Worst case just name it "phenomenon X" where X is the first unused integer.

I can find lots of examples of people naming things that don't exist. See phlogiston and ether for example, if you don't like fantasy and religion.