A research paper that recently came out suggests that deep-sea life does have a circadian rhythm, but it is regulated much differently than it is by us surface dwellers. We see light, we eat and digest, and the suprachiasmatic nucleus in the brain (our "biological" clock) keeps track of it and eventually establishes a rhythm of the circadian variety.
Most living things at the surface have some sort of circadian rhythm - the mechanisms vary, but they are present and can be readily observed.
In the deep sea, the mechanisms are quite different since they can't see any light, but the rhythm is still established. When these animals (squid in the research) eat a certain type of bacteria containing a light organ, the presence of certain proteins within that organ actually trigger a change in the gene transcription responsible for encoding the protein controlling the circadian rhythm. Thus, when the squid eats, it ultimately determines what the rhythm will be. The entrainment itself actually happens by means of the light organs consumed in the bacteria.
As far as where the bacteria ultimately get there bioluminescence, there is still research to be done, although I would presume there is a mixture of downward bacterial migration and chemical generation contributing to this.
Link to the article: http://mbio.asm.org/content/4/2/e00167-13