Objects or Meshes?

I would go with separate objects.

Firstly because that will allow you to keep your code nicely separated. To stay with your example: A gun does not need to know about what type of ship it is attached to and how to move through space and a ship does not need to know the specifics of how to produce a projectile and fire at an enemy. Keeping it separate makes maintenance a LOT easier.

It will make your job easier from a modeling point of view, since you can change the look of the gun without having to worry (too much) about the rest of the ship. You also won't have to deal with nasty things like rigging and skinning if the guns are not attached to your object.

Having multiple objects will also help you with performance since unity can only cull on a per object basis. So if you have one giant mesh and see only the tip of it, unity will still have to process every single vertex within the mesh. If you keep your guns separate, unity will only render the guns that are actually visible.