Suspension of disbelief

I must say I've never had any problem with this, because I bought into the basic idea at an early age.

"If it looks like a duck, swims like a duck, and quacks like a duck, then it probably is a duck."

OK. but if it wears cloths, rides horses, drives cars and works for a living, then it probably isn't a real duck but a surrogate-human-being. Although designed as anthropomorphic barnyard animals, Mickey and the gang were never really animals - they all walk on their hind legs, they have hands with opposable thumbs, Donald can't fly, Goofy never tries to bite car tires and Mickey was never in danger of being eaten by a cat (with the possible exception of While the Cat's Away, a remake of the Alice short Rattled by Rats, where Mickey and Minnie are part of a gang of mice whooping it up in Tom Cat's house - are there any other films where Mickey is actually mouse-size?)

This was not a concept invented by the movies, it was already established in the comic strips - Krazy Kat being the prime example - but the animated cartoonists ran with it. Audiences respond to stories about human nature - that way we know what to expect from the flow of events: nothing else makes enough sense to maintain our involvement. But funny animals are more appealing than cartoon humans, easier to draw and free of inherent stereotyping - by which I mean that a cartoon human is immediately a specific type of human (a thin man, a fat woman, fair-haired or dark-haired, a specific age, a specific race - a human character is limited by delineation!) whereas a animal can represent types common to all races and classes of human society - we can all instantly identify with them, without exclusion. (And yes, it goes back to Aesop - and probably further!)

These cartoon animals are the equivalent of the live-action silent comedians - they are "the child within" (usually more specifically an eight-year-old boy) causing innocent mayhem as they play at being adults. They were adolescents in those days before the invention of "teenagers", when you moved straight from child to adult.

It follows that if these characters are really surrogate humans, then they will have pets, eat what humans eat, etc. They have to.

So when that tiresome pedant, the super-ego, pops up to ask "how can Goofy treat Pluto as a pet when he is a dog himself?" just beat it down with your id and remind it that Pluto is meant to be a dog - and Goofy isn't! He's meant to be a human!

There was mention made on another site that all the characters in Don Bluth's The Secret of NIMH are articulate ... except the farmer's cat, Dragon. The mice speak; the rats speak (except Brutus); Jeremy the crow speaks, as does the girl crow at the end; even the Great Owl gives advice to Mrs. Brisby. Only Dragon says nothing except for horrific growling, which from a mouse's perspective is like watching a T. Rex roar at you. So, why is the cat a speechless complete monster while the film's archvillain, Jenner, is masterfully articulate? Of course, this is Fridge Logic; in the film itself, Dragon's role as Mouse Death Incarnate works perfectly.

Well, in Donald Duck's case, tailoring pants to a duck's physique would be a nightmare, so going without is no great stretch. However, going with a jacket / shirt / wifebeater or something makes him unclothed. This is fine for Zootopia's Mystic Springs Oasis, but not so much among the general public. Hence, the modesty cross. Save the au naturel for Daisy.

As for Minnie going all girly over an actual mouse: it's clearly a Medium Awareness gag. Mouse meets mouse, and somebody goes off the rails. A similar gag mechanism exists in Fantasia 2000, with Donald Duck eying a pair of Nearly Normal Animal ducks waddling onto Noah's ark.