Per sources of the Wall Street Journal, Nintendo is concerned about being seen as greedy by consumers, and actively tells its partners - including DeNA and CyberAgent - to adjust games so that players don't spend too much.
As for why a publicly listed company would try to make less money, a Nintendo employee apparently told WSJ that the company sees smartphone games more as advertising for its core console business than a straight moneymaking opportunity
This policy seemingly doesn't go down too well with some of those partners. Dragalia Lost developer CyberAgent was asked to change the game's odds of earning rare characters following player complaints.
“Nintendo is not interested in making a large amount of revenue from a single smartphone game,” a CyberAgent employee told WSJ. “If we managed the game alone, we would have made a lot more.”