So for example niche is split over three sections, dog bowls, cat bowls and hamster cages.

Should I split up into 3 EMD niche sites:

dogbowls.com
catbowls.com
hamstercages.com

OR

get a brandable domain such as PetSupplies.com and then make:

PetSupplies.com/dogbowls
PetSupplies.com/catbowls
Petsupplies.com/hamstercages

How much harder is it to rank the petsupplies website or is it pretty much neglible..?

buy all, always buy the EMD, and if you think if you can brand it, also buy the brandable domain
build them all separately and profit from all