The WeakSet is supposed to store elements by weak reference. That is, if an object is not referenced by anything else, it should be cleaned from the WeakSet.
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Let me answer the first part, and try to avoid confusing you further.
The garbage collection of dereferenced objects is not observable! It would be a paradox, because you need an object reference to check if it exists in a map. But don't trust me on this, trust Kyle Simpson: https://github.com/getify/You-Dont-Know-JS/blob/1st-ed/es6%20%26%20beyond/ch5.md#weakmaps
The problem with a lot of explanations I see here, is that they re-reference a variable to another object, or assign it a primitive value, and then check if the WeakMap contains that object or value as a key. Of course it doesn't! It never had that object/value as a key!
So the final piece to this puzzle: why does inspecting the WeakMap in a console still show all those objects there, even after you've removed all of your references to those objects? Because the console itself keeps persistent references to those Objects, for the purpose of being able to list all the keys in the WeakMap, because that is something that the WeakMap itself cannot do.