I Fly an advanced escort vessel, and on my alt i have a t2 science vessel. On my escort my cannon shots always come from my warp nacelles. on my science vessel I occasionally equip dual beam arrays, they also shoot out from the warp nacelles.
Please. Please. Please. Please. Please. Take the weapon hard points off the warp nacelles on Federation ships. They do not belong there. They should be firing from somewhere on the saucer, The Dervish fires its cannons from the saucer and it looks great doing so.