Should storm windows be removed if AC will be on and windows rarely opened?
It's an intriguing question. On one hand, trapped air is heated through radiation. On the other, it acts as an insulator. Keep in mind that we aren't talking about airflow, but heat flow (by conduction, convection, and radiation). 

The answer probably depends on how many of your windows are exposed to the sun, where extreme temperatures are generated between panes. In those cases, the insulation benefit of the second pane is probably outweighed by the efficiency lost due to greenhouse effect. 

For those windows which are usually shaded, the second pane creates a trapped-air buffer, which dramatically reduces conduction loss. 

I don't think a conclusion can be drawn with the information given. You might update your question to describe the building and property features in more detail. (Don't put it in a comment.)