Most of the distances involved in the EK route network are pretty long, which makes it impractical to have a smaller, short-haul fleet. Besides, in the Middle East there is a high demand for premium classes, including F, which means that you need to have them available even on shorter routes.
Besides, like you said, there aren't all that many flights to places like BAH, KWI and DOH, so you might lose more than you gain by operating A320s or something as well. Can you imagine a three-class A320? Could be a little tough.
The main point is probably that EK doesn't have to make money though. The whole idea behind the airline is to bring people to DXB so they can spend money there, and they do rather a good job of that IMHO. This means they can do a couple of rather unusual (if not insane) things with their fleet (like ordering 45 A380s).
15 people on a 330? Man, boarding must have been a dream.