1/6th of Panthers are also in black, and 2/6ths have black color identity. Chipmunks and squirrels transmit disease, but aren't in Black. Animals are put into black because because they are seen as bad or evil and for no real deeper reason than that. But it happens that a lot of animals we consider evil are the ones that we've historically known to transmit disease.
Panthers have a reputation for being loners and being sneaky/sly/pouncey. That's black-ish.
Chipmunks and squirrels don't have a reputation for spreading disease like rats do. They also have a reputation for mostly eating nuts, they aren't seen as critters that eat out of your trash and mess up the stuff inside your house (even if they actually might).
I would say the vast majority of color pie choices are deliberate, but you have to approach it from understanding that how we perceive or culturally understand an animal's nature is different from how they actually are. Then understand that the color choices are based on our perceptions, and not the reality.
Also, Medieval Nobility also participated in regicide, infanticide, and betrayal as a matter of course. So that just kinda enhances my point.
This doesn't take away from their white nature, it just adds black nature. There's a reason that a lot of the brutal authority figures in Magic dip into the combination of white and black.