For example, if I had a Female Zorua and bred it with a Ditto, would the offspring have any (excluding the usual differences in Pokemon breeding i.e EVs/Nature differences) difference than if I had a Male Zorua and bred it with a Ditto?
For Generation VI onward, if the female Pokémon has a non-Hidden Ability, there is a 80% chance that its offspring will have the Ability in the same slot as the mother (regardless of whether it was bred with a male Pokémon or Ditto).
In Generation VI, the Poké Ball of the female Pokémon is always passed down to its offspring (even when bred with Ditto); male and gender-unknown Pokémon have no effect on their offspring's Poké Ball in this generation.
source I think these are the only 2 differences, but the article was long and I might have missed some others.
Like McRib said it doesn't matter the gender the offspring will get normal results just as breeding with a male and a female Zorua.