We have them in our stories, and we don't really have objections to it. Sorting out the raw creature definitions is a mess.
Is it possible to sort out the raws in such manner as half-breeds can be generated as the game goes? Half-elves, half-dwarves, or however you have chosen to split races/species.
I'm going off the cuff here- I'm not privy to the code- but I suspect that while it might be a relatively simple project to compare two creature raws as they are now and then just average out/combine raws, and maybe roll randomly to select from conflicting possibilities... doing this in a way that usually produces satisfying outcomes might require a more complex RAW notation so that notable features from a race are preserved well while avoiding such sillyness as a half-elf inheriting a pair of arms from its elven mother, and pair of arms from its human father, coming out of the process looking like a badly-designed spider.
At the same time, wings are limbs, and when you have eagle-men, those guys might work best with arms AND wings, even though that technically makes them six-limbed.
Certainly some interesting challenges. However, I like the idea that animal-men and half-breeds might exist naturally in the game world. It would give animal-men more connection to the world if they are definitively tied to a certain event centuries ago.