Yes and no. You can switch between cannons which means they all have to be capable of being use just as effective as the other canons, however they can be used for different things. We were thinking along the lines of; one the cannons stuns or one of them siphons health, things like that.
But, the primary weapons such as machine guns and missiles that use different buttons to fire than the cannons use, have permanent upgrades (3 for each).