Why do the average number of stomata differ in between plant species?

Answer 1

One reason is climate. Desert plants have less stomata than other plants as they tend to lose moisture when they absorb carbon dioxide, and expel oxygen. Some desert plants have their stomata on the underside of the leaf. Many of these plant's stomata open only at night and close during the day. The carbon dioxide is temporarily chemically "attached" to an organic molecule, (I don't remember which one), and during the day the carbon dioxide is freed for photosynthesis.
Good question.
Doc. Dan.

Answer 2

Basically going with Dan. The plant needs to keep stomata open to exchange gases with the outside air (so more is better) but for a plant in a dry climate, more can lead to huge water loss and be disastrous, so dry climate plants have fewer stomata, and they may be protected from water loss by ridges or hairs. Plants like water lilies which have leaves on the water surface have no stomata on the bottom surface - oxygen and CO2 are exchanged directly between surface cells and water.