There is no definite answer to it as we have two eyes, two ears, one mouth etc.
But it may be due to the nasal cycle. For example, when we smell, there is a chemical reaction in the olfactory receptors. So, if we would have one nostrils, we could not get to know the smell is strong or weak. Another reason may be of nasal cycle.When we breathe predominantly through one nostril at a time, and the other side becomes a bit congested and rests and we will probably find that one becomes stuffier than the other.
The top side of our nasal cavity is directly under your brain & is separated from it by a very thin wall of bone & mucus membrane.