I'm not a science-y person butttttttt...

It seems like the less orifices we have the better. It cuts down on the risk of things like foreign objects and bacteria invading our bodies. If you think about it, we only have eyes, ears, nose, mouth, pee hole, and poop hole. (I realize the vagina is technically not a pee hole but let's call them one in the same for now, since they are right on top of one another.) They all use things like hair/mucus/tears to protect them as much as possible.

The systems of the body that use these things have pretty much combined as many of the holes as possible (ie breathing/eating), while still being optimized for their use. It wouldn't be as practical to hear through the nose because we get omnidirectional sound by placing them on the sides of our heads.

Our digestive system leads out in the most efficient way and a pee hole on the bottom of our foot would require a lot more tubing.

If you look at it like that, deciding to piss out of the reproductive organ isn't as weird. There's already a hole that isn't used to much. May as well use it instead of figuring out how to create another hole and protect it.

edit: This is fun. I don't think it is possible to smell through our ears because of the (1) sound air moving makes across the eardrum (2) the pressure in our ears that maintains our balance wouldn't work either. Smelling through the eyes could be interesting. The sensory stuff that allows us to smell could have a smaller tube placed in the inner section. Probably mess up how wet/dry our eyes are.

I wonder if this has something more to do with the evolution of organisms in the water originally. Most of them have sealed eyes right? But they still have nostrils?