Lord tyrius, your idea makes me think of a side arm in an fps. Rather then reload you pull out the secondary weapon and then reload both.
@sypheria, could this benefit be "simulated"? Players could program ahead of time to either "use" both (or however many sides the ship has) sides ammunition or not. The effect being if you select "both" then there is a shorter then normal reload (one fore every side of the ship with guns) then once that counter is up the reload time is longer then normal. If that makes sense? Is it too much overly complicated?
Edit: also how do missiles work? Wouldn't missiles that are guided be able to be fired from all sides at once at the same target? Wouldn't the firing arc mean nothing to missiles, all that would matter would be range