While they do help improve aerodynamics slightly, it has a decent benefit to "cold" starts. So like mentioned before, it does help emissions. Because when your truck starts "cold" ('cold' meaning not warmed up fully, not necessarily 'cold' ambient temperatures), the combustion and catalyst doesn't burn the normal greenhouse gases that it would as if it were fully warmed up. The shutters reduce air flow, allowing less airflow over the engine hence allowing the engine and other components to warm up quicker. Plus you can get quicker catalyst light off. So you not only reduce emissions, but you also increase fuel economy because you heat up quicker. Coolant heats up quicker which heats up your engine oil quicker, which then sends coolant to your trans. heater quicker. While you probably wont see your fuel economy number go down much after removing the shutters, you may notice time to warm up take longer.
While at FCA, I remember trying to completely seal the engine compartment so we could heat up much quicker. Like crazykid1994 said, the hotter you can run the engine, typically the happier it is (well, if it was designed to handle the heat load and not crack the block
). But the downside is making sure you can keep it cool for towing requirements.