Clojure is written in java (and clojure). It uses bit operations to implement Software Transactional Memory and persistent collections. Is it a bad code?

You seem to think a programmer should always code on the same level of abstraction. I'd argue in many applications often you find no suitable abstraction, and have to implement it yourself.

Also linear feedback shift registers can be used without any knowledge about bits other than the fact that integers loop over when they reach maximum value (and every programmer should know that anyways). And these registers are useful for some very nice algorithms (like in-place pseudorandom permutations' generators - for example for shuffling songs in a media player, or for some ai algorithms).