I would say "Tell me how it's going" or "So how is it going?" to someone who has recently started a new job and you want to know the current situation.
"Tell me how it goes" or "Let me know how it goes" is one of those instances where the present tense indicates the future. I would say that to someone before they have, for example, a job interview to indicate that I want them to call me once it's over and tell me what happened. I would not use it to indicate a query about the present situation.