Another place where you find rats is in the Desert place. You know, where the Mirror of Twilight is?
While in there, there are invisable rats that you need to use your senses to see them.
I haven't been to the Cave of Ordeals yet. Do you have to go there during your mission thing? Because if so, I haven't been there and I am at the last part of the game, in Hyrule Castle.
I really need to get to the CoO because I haven't been there yet and I want to know what it's like. If there are lots of rats, like what Sparx said, then I might freak out! I do not like rats!