Que can be used in several different contexts and come in different grammatical flavors. It can be a relative pronoun (with or without ce) and also a conjunction, starting a relative clause.

Starting with que as simple relative pronoun:

Mon père me raconte des histoires, que j'aime. -- My father tells me stories, that I love.

Que refers to the particular stories, which the father tells her.

Ce que, on the other hand,  refers to an abstract idea, often mentioned in a different sentence, and not to a specific noun in the same sentence.

Mon père me raconte des histoires, ce que j'aime. -- My father tells me stories, which is what I love.

Que can also start a new relative clause:

J'espère que tu vas bien. -- I hope that you're well.

In this case, que does not refer to any noun.

And the same case with the sentence: "Ça fait 30 minutes qu'on attend notre table."

Yes.