Strange, I laughed at those jokes in Zootopia. The bunnies line is just a reflection of Judy’s issue with being thought of as just a defensless little bunny. You’re reading far too much into it.
I’ve tried to warm up to Secret Of NIMH over the years, but Bluth took too many liberties with the source material, which I read and loved back in the 5th grade. None of that mystical mumbo jumbo is in the book, and the rats do not dress like they’re at a Ren Fest. The rat’s whole backstory would have made a film in itself, and got way more time in the book as well.