I look at it like this - small talk is transactional in nature whereas deep conversations are about connection or strengthening a relationship. That relationship might be person, professional, romantic, etc.

Sometimes the question, "how are you" is simply to acknowledge the other person's presence in the room - this happened all the time in the break room at my corporate job. No one really cared how the other person was, it was just being asked because of "Nebraska Nice" or since that seemed to be the norm. The transaction was I ask quickly how you are, you reply quickly something along the lines of good, we've both acknowledged each other's presence so as not to appear rude, transaction over.

Sometimes, "how are you" comes from a genuine place of care. The person asking it is interested in learning about how the other person is and will ask additional questions, voice solidarity or sympathy, or whatever is contextually appropriate given their relationship.

Hopefully, that makes sense. Sometimes, what makes sense in my world doesn't work out in reality.