What % of NYT readers voted for Trump? It has to be minuscule.
The election was so close, there are dozens of but-for causes that could have tipped the scale, but the NYT not being sufficiently alarmist about Trump (which is what that CNN article you linked claims - not that the paper was a proponent of Trump, as you say) probably wasn’t one of them.

You’re right, they look better as sixes. It’s just a goofy font.