If the showrunners' were truly upset that Hillary lost, they would have made Baker the alien President and Marsdin the human vice president. Making the female president an alien with the illegitimate claim on the office would be a slap in the face of a Hillary presidency and a dog whistle to the alt rights to further descry the 1st female American presidency on our world.
I think they would have gone in another direction had Hillary won. I think their hatred of Trump drives their show.
... then again so would Riverdale, Supernatural and The Flash.
Maybe, but notice that Supergirl's decline is higher than the three shows you mention, and its ratings are about half of the Flash's in the 18-49 demographic, despite airing on the most watched night of the week.
What frustrates me most is that I think Supergirl could be the best of all of them with a creative team that cared more about telling hero stories than campaigning against Trump.
Ignoring the crossover, I don't think there was any episode better on all 5 shows that was better than the Lex two parter earlier this season. I don't know how the storyline will end the finale, but that two parter was top level stuff.