Is it some self punishment for something?

nothing in the film would suggest that hirayama views his job as bad, unpleasant, or unfulfilling. he seems attached to routine and the job he works allows for a degree of regularity, predictability, and simplicity he seems to value very much.

even his sister was very surprised.

considering the sister was chauffered to his apartment in the backseat of a luxury vehicle, i'd venture to guess she was surprised because their family is well-off and hirayama is voluntarily living well below the standard of living for the rest of their family. his sister also mentions their father is in a nursing home (which i assume is not cheap). she's incredulous her brother would choose to clean toilets instead of performing more "dignified" work.

Why he cried when niece left?

i think this isn't so much because niko left, but rather because he hasn't seen his sister in a long time and has been reminded of his past and his family members (with whom he doesn't seem to have had very pleasant relationships).

Also why cry in the very last scene driving into dawn?

compared to his usual quiet and peaceful routine, hirayama has had a lot of highly-emotional experiences recently (both happy and sad); it makes sense it'd build up over time. however, i also i think this scene is very metaphorical. he's going through weeks' worth of emotions in a couple minutes--from neutral to happy to sad to tearful and back to happy again. i think the filmmakers wanted to highlight that life isn't always sad or always happy; we cycle through moods and pleasant/unpleasant experiences all the time, but every day will eventually end and a new one will come.