"Not the brightest crayon in the box, star in the sky" etc.?

I think they make sense AND are ironic! They're examples of a combination of two figures of speech, metaphor and litotes. Metaphor you already understand--an implied comparison by calling one thing another. Litotes (pronounced LIT o tees) is ironic, usually negative, understatement. It's particularly characteristic of English and has been for over 1000 years. In Hamlet, when Rosencrantz (or guildenstern) says, "On Fortune's cap we are not the very on," he means that their luck is actually pretty bad. We see it in everyday use when we say "Not bad!" about some outstanding achievement. So when we say someone is not the sharpest crayon in the box. we're using metaphor by calling that person a crayon, and we're using litotes by putting it that way when we really mean he's downright slow!