This is where simpler, more abstracted art styles come in. Show-style gets away with it because it's a style which people normally don't look closer and realize how silly it is. Instead, I realize they probably made the nose like that to get away with smaller mouth and nose, much like actual cartoonists have great freedoms with regular anatomy to create more interesting characters. More realistic styles depend on better understanding of actual anatomy since people are gonna look at those more literally.
I think my avatar (at the time of writing for anyone who reads this comment in the future) shows where I am at with coping with non-sensical form with 3/4 noses. I find that it's largely trial-and-error but with the understanding that noses should be kept small and the shape should probably should not try to stray too far away from show-style at the same time.
For the most part, the best approach to figuring out this problem is just... do your anatomy homework. Learn from anatomy of both horses and humans.