Zelda is trademarked

Edit: Also, it's a bit more complicated in terms of IP, but it is relevant to future works.

For example, fictional characters.

Let's take Mickey Mouse as an example. Steamboat Willie is entering public domain, so the protections on the character as defined in that work is entering the public domain. But characterization of the figure in works still under copyright that have added unique details are still protected.

But the test for infringement of a fictional character is twofold. (1) Can the figure be copyrighted? (2) Is there infringement of unique characteristics?

That second part becomes much more difficult to enforce if you've been allowing millions of variations of your protected character when you initial work defining the character is no longer enforceable.

So if LoZ on the NES enters the public domain making 'Ganon' as a pig usable by people, but since that game there's been tons of spinoffs by others having Ganon as a human before Nintendo had Ganon as depicted in OoT, then they'd have a much harder time enforcing copyright on Ganon being depicted as a human even if Ganon as a pig was no longer under copyright.

No lawyer is going to say "yeah, let 3rd parties use your IP willy nilly, I'm sure it will be fine and not bite us in the ass later on."

For example:

Copyright protection is effectively never lost, unless explicitly given away or the copyright has expired. However, if you do not actively defend your copyright, there may be broader unauthorized uses than you would like. It is a good idea to pursue enforcement actions as soon as you discover misuse of your copyright protected material.

• Copyright Myths

Edit 2: Or the statute of limitations:

If you have experienced copyright infringement, you have the right to pursue a lawsuit. However, you only have a limited time frame during which to file a claim. This legal principle is called the “statute of limitations.” Ensuring that you file a claim to enforce your copyright within the statute of limitations is crucial. If you wait too long, you will lose the right to enforce your copyright and obtain your deserved damages.

• Source

So a fan project that you don't enforce against for three years which eventually monetizes as competition without infringement trademarks would be a potential concern.