My skills are Starship Energy Weapons 9, Starship Cannon Weapons 9, Starship Projectile Weapons 4.

Then Three Heavy Dual Cannons / Two Heavy Dual Cannons + One Torpedo Launcher / Two Heavy Dual Cannons + One Dual Beam Bank. <- Which one is most efficient to do DPS in my case?

Well, I was using three heavy dual cannons(with my Escort ship & Cannon : Rapid fire skill), but I felt Firing cooltime between each cannons bothered to do dps properly. Surely, there's no numerical evidence for proving it. Did I delude myself?

if you only use two heavy cannons there will be a slight delay between firing the second set and firing the first again, having three gets rid of this delay but leaves the first set ready for at most a second before you can fire it. the dual beam setup works well enough though to max that out you may want to put points into beam weapons as well.

Personally though I'd go with two heavies and a torp, preferably quantum. A well placed high yield after the cannons **** a shield facing can be devastating.